Selenoproteins discussion

DI1

The DI1 protein is found in the scaffold KI537096.1 between positions 13372651 and 13372307. The hit of the query sequence is in the negative strand. The gene encoding the selenoprotein contains 4 exons and 3 introns. A single Sec residue was found in exon. 2

Despite having compared this protein in both human and dolphin, the dolphin protein is the one that has a higher percentage of similarity (96.52%). Therefore, the results shown correspond to the predicted DI1 protein comparing it with the dolphin. Thus, we can conclude that this protein is conserved in all three species.

Finally, an A grade SECIS element was found between positions 86327 and 86257, located in the 3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

DI2

The DI2 protein is found in the scaffold KI538108.1 between positions 3922741 and 3922121. The hit of the query sequence is in the negative strand. The gene encoding the selenoprotein contains 1 intron and 2 exons. A single Sec residue was found in exon 2.

Despite the comparison of DI2 and both human and dolphin homologous, the dolphin’s protein has a higher percentage of similarity (90.82%). Therefore, the results shown correspond to the predicted protein DI2 if compared with dolphin. In conclusion, we can say that this protein is conserved in all three species.

Finally, an A grade SECIS element was found between positions 95206 and 95134, located in the 3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

DI3

The DI3 protein is found in the scaffold KI537651.1 between positions 13310335 and 13309538. The hit of the query sequence is in the negative strand. The gene encoding the selenoprotein contains 1 exon and none intron. Only one Sec residue was found.

Although the whale’s protein was compared with both human and dolphin, dolphin is the one that has a higher percentage of similarity (98.08%). Therefore, as in the previous cases, the results correspond to the predicted DI3 protein of minke whale if compared with dolphin. However, this protein does not start with Met, but if compared with human this amino acid is observed right before the phenylalanine amino acid comprising at first. Thus, we can conclude that this protein is conserved in all three species.

Finally, an A grade SECIS element was found between positions 99386 and 99306 and it was also located in the 3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

GPx

The GPx selenoprotein is located in the genome scaffold KI537586.1 between positions 2116987 and 2116838. The hit of the query sequence is in the negative strand. The gene encoding the selenoprotein contains 4 exons and 3 introns. A single Sec residue was found in exon 1.

This protein was compared with the dolphin one in order to predict its sequence, as humans do not have any. It is a protein family of glutathione peroxidases whose specific function has not been described. However, it has a high similarity with the dolphin GPx protein (96%).

The predicted protein is localized in the same scaffold as GPx2 and GPx4, but all are in different positions. Thus they are different proteins.

Many scaffolds were obtained, and it could have different explanations. This may be due to the fact that this family of proteins contains many proteins with similar sequence and the hits obtained correspond to another type of proteins of this family.

Finally, an A grade SECIS element was found between positions 99490 and 99419, located in the 3'UTR region  of the gene described above.

GPx1

The GPx1 selenoprotein is located in the genome scaffold KI537319.1 between positions 1939406 and 1939762. The hit of the query equence is in the positive strand. The gene encoding the GPx1 selenoprotein contains  1 intron and 2 exons. A single Sec residue was found in exon 1.

Despite having compared this protein of minke whale with both dolphin and human sequence, the human GPx1 is better annotated and begins with a Met residue. Therefore, the results previously shown correspond to the alignment between minke whale and human GPx1 proteins. However, we can conclude that GPx1 is very similar in all three species, preserving most of the amino acids sequence.The sequence does not start with Met in minke whale, so the whole GPx1 protein could not be predicted.

Many scaffolds were obtained. This may be due to the similarity of the proteins’ sequence within the same family or the different correspondence between hits and proteins.

Finally, an A grade SECIS element was found between positions 100408 and 100482, located in the 3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

GPx2

The GPx2 selenoprotein is localized in the genome scaffold KI537886.1 between positions 2203774 and 2203352. The hit of the query sequence is in the reverse strand. The gene encoding the selenoprotein contains 1 intron and 2 exon. A single Sec residue was found in exon 1.

The predicted protein is localized in the same scaffold as GPx and GPx4, but all of them are in different positions. Thus, we can say they are different proteins.

Although this protein was compared with both human and dolphin, the results shown correspond to the predicted protein compared with human because, in this case, we get the entire sequence since it begins with a Met residue. However, GPx2 is very similar in all three species.

Many scaffolds were obtained. Like in the previous case, this may be owing to the similar sequence that many proteins of this family show or to the allocation of the hits obtained to other proteins within the same family.

Finally, an A grade SECIS element was found between positions 99785 and 99721, located in the 3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

GPx3

The GPx3 selenoprotein is situated in the genome scaffold KI538108.1 between positions 903583 and 903401. The hit of the query sequence is in the negative strand. The gene encoding the selenoprotein contains 5 exons and 4 introns. A single Sec residue was found in exon 1.

An alignment has been done with the GPx3 of horse to predict the sequence since the the dolphin does not have it, and in humans there are differet sequences for this selenoprotein. The observed similarity with horse is sufficiently high (91.84%) but could not predict the entire protein as the first amino acid is not Met.

These results suggest that the minke whale may have a selenoprotein that is not found in dolphin.

Many scaffolds were obtained. Like in the previous case, this may be owing to the similar sequence that many proteins of this family show or to the allocation of the hits obtained to other proteins within the same family.

Finally, an A grade SECIS element was found between positions 99360 and 99285, located in the 3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

GPx4

The GPx4 selenoprotein is located in the genome scaffold KI537586.1 between positions 2117264 and 2117118. The hit of the query sequence is in the negative strand. The gene encoding the GPx4 selenoprotein contains 6 exons and 7 introns. A single Sec residue was found in exon 3.

The results shown correspond to the predicted protein compared to human as, in this case, the GPx4 protein of dolphin does not contai a selenocysteine residue. This allows us to state that, unlike dolphin, the minke whale has acquired a new selenoprotein. In addition, the entire protein was predicted as the first amino acid of the sequence is Met and it has a 91.8% of similarity with the human one.

The predicted protein is localized in the same scaffold as GPx and GPx2, but all three are in different positions. This results allow us to afirm that they are different proteins.

Many scaffolds were obtained and like in the previous case, it may be due to the existence of a certain number of protein with a similar sequence in the GPx family and to the fact that the hits conrrespond to other types of proteins of this family.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

GPx6

The GPx6 selenoprotein is located in the genome scaffold KI537663.1 between positions 1151445 and 1151233. The hit of the  query sequence is in the negative strand. The gene encoding the selenoprotein contains 5 exons and 4 introns. A single Sec residue was found in exon 2.

Despite having compared this protein with in both human and dolphin, the results shown before, correspond to the comparison between the human and the minke whale GPx6 proteins. However, this selenoprotein is pretty similar in all three species, preserving most of the amino acids. The amino acid sequence has not been found since the first complete amino acid is not Met, but by observing the T-Coffee only the first 3 amino acids need to be predicted.

Many scaffolds were obtained. As previously mentioned, this may be caused by the similarity among sequences of proteins of the same family and due to the correspondence of the hits to other proteins of this family.

Finally, a C grade SECIS elemnent was found between positions 99450 and 99375, located in the 3'UTR region of the gene described above.

Sel15

The Sel15 selenoprotein is localized in the genome scaffold KI537467.1 between positions 4339730 and 4339933. The hit of the query sequence is in the reverse strand. The gene encoding the selenoprotein contains 5 exons and 4 introns. A single Sec residue was found in exon 3.

Despite this protein was compared with both human and dolphin, the dolphin’s protein has a higher percentage of similarity (88.24%) with minke whale’s Sel15. Therefore, the results shown correspond to the predicted protein Sel15 of minke whale compared to the dolphin one. However, we can conclude that this selenoprotein is very similar in all three species, preserving most of the amino acids sequence.

Finally, an A grade SECIS element was found between positions 71763 and 71686, located in the 3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

SelH

The SelH selenoprotein is loalized in the genome scaffold KI538536.1 between positions 7335258 and 7335614. The hit of the genome sequence query string is postive. The gene encoding the selenoprotein contains 2 exons and 3 introns.  A single Sec residue was found in exon 2.

Although this protein was compared with both human and dolphin, dolphin’s protein has a higher percentage of similarity (73.11%) with the minke whale’s protein. Therefore, the results shown correspond to the predicted protein SelH of minke whale compared to the dolphin one. However, SelH is very similar in all three species and conserves most of the amino acids.

Finally, an A grade SECIS element was found between positions 101361 and 101427, situated in the 3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

SelI

The SelI selenoprotein is located in the scaffold KI538253.1 between positions 1519374 and 1519646. The hit of the query sequence is in the forward strand. The gene encoding the selenoprotein contains 10 exons and 9 introns. A single Sec residue was found in exon 10.

SelI is not a selenoprotein in dolphin, as it does not have any Sec residue. So, the human SelI selenoprotein was used as a query, which contains a Sec residue. Thus, the identification of the SelI selenoprotein of minke whale was possible, showing a high similarity with the human one (94.51%). Acording to the results obtained, SelI is conserved in these two species (human and minke whale) and dolphin has lost it or maybe it isn't annotated.

Finally, an A grade SECIS element was found between positions 113709 and 113786, situated in the 3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

SelK

The SelK selenoprotein is located in the scaffold KI537537.1 between positions 1963592 and 1963488. The hit of the query sequence is in the negative strand. The gene encoding the selenoprotein contains 5 exons and 4 introns. A single Sec residue was found in exon 4.

Despite having compared this protein with both human and dolphin, dolphin has a higher percentage of similarity (88.57%) with the minke whale. Therefore, the results shown correspond to the predicted protein Selk of minke whale compared to the dolphin one. However, this selenoprotein is  well preserved and very similar in the three species.

Finally, an A grade SECIS element was found between positions 97399 and 97312, but this is localized in the fourth intronic region. However, it was considered that this SECIS element could be correct as there are only two nucleotides corresponding to the STOP codon (TGA) of the protein in exon 5.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

SelM

The SelM selenoprotein is located in the scaffold KI537401.1 between positions 805341 and 805502. The hit of the query sequence is in the positive strand. The gene encoding the selenoprotein contains 5 exons and 4 introns. A single Sec residue was foun in exon 2.

This protein was compared with both human and dolphin. The dolphin’s protein has a higher percentage of similarity (96.30%) with th minke whale’s protein. Therefore, the results shown correspond to the predicted protein SelM of minke whale compared to the one of dolphin. In this case, although the SelM selenoprotein is conserved in all three species, there is a fragment of the dolphin protein that is not predicted, but in the minke whale matches up to the human seuquence as shown in the multiple alignment.

Finally, an A grade SECIS element was found between positions 100196 and 100268, situated in the 3'UTR region of the gene described above. It is important to emphasize that, in this case, two residues of the apical loop are both Cytokines (CC).

SelN

The SelN selenoprotein is located in the scaffold KI537648.1 between positions 939264 and 939136. The hit of the query sequence is in the negative strand. The gene encoding the selenoprotein contains 10 exons and 11 introns. A single Sec residue was found in exon 8.

Despite having compared this protein with both human and dolphin, dolphin is the one that has a higher percentage of similarity (95.35%). Therefore, the results shown correspond to the predicted SelN protein comparing it with dolphin. However, this protein does not begin with Met like the dolphin protein, and therefore it could not be predicted at all.

Finally, an A grade SECIS element was found between positions 919334 and 91867 located in the  3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

SelO*

The SelO protein is localized in the scaffold KI538131.1 between positions 939264 and 939136. The hit of the query sequence is on the forward strand. The gene encoding SelO contains 10 exons and 11 introns. No Sec residue was found.

This protein has been compared to human, dolphin and horse. The human SelO contains a Sec residue in the last exon like the horse does; however, the dolphin does not have SelO. The results obtained show the predicted SelO protein in the minke whale compared to the one in horse. In exonerate, there is a very good alignment between these two sequences except for the last exon, where only 6 amino acids out of 12 are conserved. However, as observed in the T-Coffee, the entire exon was not predicted in the minke whale. Actually, the part which contains Sec in horse is left.

On the other hand, an A grade SECIS element was found between positions 100767 and 100844,  located in intron 10 where the two conserved residues of the apical loop are two Cytokines (CC), like in SelM.

Based on these results we can conclude that SelO may not be considered as a selenoprotein since no Sec residues were found, as in dolphin and unlike in human and horse. Different possible scenarios could exist. One would be that the minke whale may have lost a Sec residue, even if it still keeps the SECIS element, or that it has never had it.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

SelP

The SelP protein is located in the scaffold KI5388471.1 between positions 3715058 and 3714792, in the negative strand. The gene encoding SelP contains 4 exons and 3 introns. 14 Sec residues were found in the predicted protein of minke whale.

The minke whale genome was compared with dolphin, human and horse SelP. The human protein contains 10 selenocysteines, still, the dolphin one contains a unique Sec residue because its sequence is incomplete. Regarding the SelP of horse, 13 Sec residiues where found within its genome.

Due to this variation in the number of selenocysteines, it was proceeded to perform a quadruple alignment with the species mentioned above. Only one Sec residue was found in all 4 species, 9 selenecyteines were recognized as conserved residues in minke whale and human, and 12 in minke whale and horse. Nevertheless, two Sec residues were observed in minke whale that none of the other species had.

The results shown correspond to the minke whale’s SelP protein predicted by comparing it with the human one. In exonerate, a good alignment was observed and it was possible to identify Cys residues in the human sequence whereas the whale had new TGA codons.

From these results we can conclude that the predicted SelP of minke whale contains several Sec residues in all species but their number varies. This may be because not all residues are important for the function of this protein.

Finally, two A grade SECIS element were found between positions 94707 and 94625, and 94248 and 94183; both located in the 3'UTR region of the gene described above.

SelR1

The SelR1 selenoprotein is located in the genome scaffold KI537749.1 between positions 5903631 and 5903786, in the positive strand. The predicted gene encoding SelR1 contains 3 exons and 2 introns, and a Sec residue was found in exon 3.

The same hit was found through the alignment of the sequence and the protein SelR1 of dolphin and human. This indicates that the sequence of the SelR1 selenoprotein is widely conserved in all three species. However, there is a higher level of sequence similarity between minke whale and dolphin, reaching the value of 98.08%, which indicates that the alignment is nearly perfect. In addition, the protein begins with a Met residue what means that the beginning of the gene was found.

Finally, an A grade SECIS element was found between positions 102044 and 102114, located in the 3'UTR region  of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

SelS

The SelS selenoprotein is found in the scaffold KI537668.1 between positions 2980583 and 2980666. The hit of the query sequence is in the forward strand. The predicted gene contains 6 exons and 5 introns. A single Sec residue was found in exon 6.

The same hit was found by aligning the selenoprotein SelS of the minke whale with the human and the dolphin ones indicating that the sequence is conserved in all three species. The level of similarity is higher when comparing with the human sequences (96.43%). Here, also, the homologous protein begins wit a Met residue. Thus, the results are shown by the alignment with this species. The whole sequence of the minke whale SelS has been predicted as it starts with Met as well.

Finally, an A grade SECIS element was found between positions 108267 and 108346, situated in the 3'UTR region  of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

SelT

The SelT selenoproteins is located in the genome scaffold KI537881.1 between positions 193734 and 194333. The hit of the query sequence is in the negative strand. The predicted gene contains 2 exons and 1 intron. A single Sec residue was found in exon 1.

The same hit was found by doing the alignment of the minke whale sequence with dolphin and human, indicating that the sequence of selenoprotein SelT is conserved in the three species. The level of sequence similarity is higher when compating with dolphin (75.5%), so the results are shown by doing the alignment with this species. It must be mentioned, however, that the predicted amino acid sequence does not start with Met either in the case of the minke whale or the dolphin. Therefore, the initial part of the protein could not be predicted.

Finally, a C grade SECIS element was found between positions 100644 and 100731, situated in the  3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

SelW

The SelW protein is localized in the scaffold KI537293.1 between positions 4165820 and 4165894. The hit of the query sequence is in the positive strand. The gene encoding the selenoprotein contains 5 exons and 4 introns. A single Sec residue was found in exon 2.

The same hit was found by doing the alignment of the protein sequence in human and dolphin. This fact indicates that the sequence of the selenoprotein SelW is widely conserved in all three species. However, the highest level of similarity is achieved with the comparison of the sequences with dolphin’s SelW, obtaining a value of 100%. In addition, the  first amino acid of the predicted protein is Met.

Finally, an A grade SECIS element was found between positions 101413 and 101496, situated in the 3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

TR

The TR protein is located in the scaffold KI537194.1 between positions 7761998 and 7761807. The hit of the query sequence is in the negative strand. The gene encoding the TR selenoprotein contains 5 exons and 4 introns. A single Sec residue was found in exon 5.

This protein has been compared with the TR selenoprotein of dolphin since it is the only animal that has it recorded. It is a protein of the tioredoxin reductase family that does not correspond to either type 1, type 2 or type 3 and has been found in different positions of the scaffold KI537194.1. This protein has not been fully predicted as it does not start with Met. So we can say that this selenoprotein is conserved in both dolphin and minke whale.

Finally, an A grade SECIS element was found between positions 73349 and 73273, located in the 3'UTR region of the gene described above.

TR1

The TR1 protein is located in the scaffold KI537194.1 between positions 7766581 and 7766342. The hit of the query sequence is in the negative strand. The gene encoding the selenoprotein contains 17 exons and 16 introns. A singlen Sec residue was found in exon 17.

This protein has been compared with the human TR1 selenoprotein because it is not recorded in dolphin. This protein has not been fully predicted since it does not start with Met, but the in T-Coffee the initial sequence can be observed.

We can say that the TR1 selenoprotein is conserved in humans and the minke whale but not in dolphin (actually, it was not found in this species).

Finally, an A grade SECIS element was found between positions 68832 and 68756, located in the 3'UTR region of the gene described above.

TR2

The TR2 protein is localized in the scaffold KI538526.1 between positions 5998784 and 5999038. The hit query sequence is in the forward strand. The gene encoding TR2 contains 17 exons and 16 introns. A single Sec residue was found in exon 17.

This protein has been compared to the TR2 selenoprotein of horse and human, since the dolphin one is not annotated. It presents a higher percentage of similarity with theTR2  protein of horse (63.53%). So, the results shown correspond to the predicted TR2 protein of minke whale compared with the horse one. It was not entirely predicted as it does not start with Met.

We can state that the TR2 selenoprotein is conserved in human  and minke whale but not in dolphin, as it was not found.

Finally, an A grade SECIS element was found between positions 102289 and 102358, situated in the 3'UTR region of the gene described above.

To know more about conservation among different species analyzed, click here to see the multiple alignment.

TR3

The TR3 protein is situated in the scaffold KI537815.1 between positions 502841 and 502987. The hit of the query sequence is in the positive strand. The gene encoding TR3 contains 16 exons and 15 introns. A signle Sec residue was found in exon 16.

This protein has been compared with the TR3 protein of human, dolphin and  horse. The results shown correspond to the predicted TR3 protein of minke whale compared to the dolphin one because, although it does not begin with a Met residue, it is the one that got the best results in exonerate; where a great similarity between proteins is noticeable. Although it is a truly good alignment (including TGA codon), in the T-Coffee,  only the first part of the sequence is kept. Also, the alignment of the two first Sec residues of the proteins are not shown.

Despite this, an A grade SECIS element was found between positions 118106 and 118174, located in the 3'UTR region of the gene described above.

On the basis of these results, we can say that, besides the T-Coffee, which we believe may have worked wrongly because of the undetermined residues that appear in the exonerate results (between positions 443 and 446), the selenoprotein TR3 of minke whale presents homology with the TR3 of dolphin.

Machinery elements discussion

eEFsec

The eEFsec protein is found in the KI537675.1 scaffold of the whale’s genome between positions 1175911 and 1175249. The hit of the query sequence is in the negative strand. The gene encoding the protein contains 6 exons and 5 introns. Any Sec residue was found in this gene.

This protein has been compared with its homologous in human, dolphin and horse finding the same scaffold in all three cases.  However, the best t-coffee alignment was with the horse eEFsec although it does not start by Met. Therefore, the results shown previously, correspond to the alignment with the horse protein. In the whale, the first amino acid is not a Met, thus, the eEFsec protein has not been completely predicted.

Finally, no SECIS element was found in the 3’ UTR region of the gene described above.

Taking into account these results we can conclude that the eEFsec of the whale, as in human, horse and dolphin, is not a selenoprotein and it is part of the selenoproteins synthesis machinery.

PSTK

The PSTK protein is found in the KI537470.1 scaffold of the whale’s genome between positions 14272944 and 14273201. The hit of the query sequence is in the positive strand. The gene encoding the protein contains 6 exons and 5 introns. Any Sec residue was found in this gene.

Despite having compared this protein in both human and dolphin, the dolphin’s PSTK sequence has more similarity (98.84%). Therefore, the results shown previously, correspond to the alignment with the dolphin protein. However, it can be conclude that the sequence of this protein is very similar in all the three species. In the whale, the first amino acid of PTSK is a Met, thus, the PSTK protein has been completely predicted.

Finally, no SECIS element was found in the 3’ UTR region of the gene described above.

Taking into account these results we can conclude that the eEFsec of the whale, as in human and dolphin, is not a selenoprotein and it is part of the selenoproteins synthesis machinery.

SBP2

The SBP2 protein is found in the KI538386.1 scaffold of the whale’s genome between positions 1254372 and 1254593. The hit of the query sequence is in the positive strand. The gene encoding the protein contains 19 introns and 20 exons. Any Sec residue was found in this gene.

Despite having compared this protein in both human and dolphin, the human SBP2 sequence is better annotated and starts by Met. Therefore, the results shown previously correspond to the alignment with the human protein. Even so, it is possible to conclude that the sequence of this protein is really similar in all the three species. In the whale, the first amino acid is a Met, thus, the SBP2 protein has been completely predicted.

Finally, any SECIS element located in the 3’ UTR region has been found.

Taking into account these results we can conclude that the SBP2 of the whale, as in the human and the dolphin, is not a selenoprotein and it is part of the selenoproteins synthesis machinery.

SECp43

The SECp43 protein is found in the KI537394.1 scaffold of the whale’s genome between positions 1637017 and 1637160. The hit of the query sequence is in the positive strand. The gene encoding the protein contains 8 introns and 9 exons. Any Sec residue was found in this gene.

Despite having compared this protein in both human and dolphin, the human SBP2 sequence is better annotated and starts by Met. Therefore, the results shown previously correspond to the alignment with the human protein. Even so, it is possible to conclude that the sequence of this protein is really similar in all the three species. In the whale, the first amino acid is a Met, thus, the SECp43 protein has been completely predicted.

Finally, any SECIS element located in the 3’ UTR region has been found.

Taking into account these results we can conclude that the SECp43 of the whale, as in the human and the dolphin, is not a selenoprotein and it is part of the selenoproteins synthesis machinery.

SecS

The SecS protein is found in the KI537300.1 scaffold of the whale’s genome between positions 2890711 and 2890427. The hit of the query sequence is in the negative strand. The gene encoding the protein contains 11 introns and 12 exons. Any Sec residue was found in this gene.

Despite having compared this protein in both human and dolphin, the dolphin SecS sequence has higher similarity (93.68%) with the whale’s one. Therefore, the results shown previously correspond to the alignment with the dolphin protein. Even so, it is possible to conclude that the sequence of this protein is really similar in all the three species. In the whale, the first amino acid is a Met, thus, the SecS protein has been completely predicted.

Finally, any SECIS element located in the 3’ UTR region has been found.

Taking into account these results we can conclude that the SecS of the whale, as in the human and the dolphin, is not a selenoprotein and it is part of the selenoproteins synthesis machinery.

SPS1

The SPS1 protein is found in the KI538175.1 scaffold of the whale’s genome between positions 11516270 and 11516270. The hit of the query sequence is in the negative strand. The gene encoding the protein contains 7 introns and 8 exons. Any Sec residue was found in this gene.

Despite having compared this protein in both human and dolphin, the dolphin SecS sequence has higher similarity (100%) with the whale’s one. Therefore, the results shown previously correspond to the alignment with the dolphin protein. Even so, it is possible to conclude that the sequence of this protein is really similar in all the three species. In the whale, the first amino acid is a Met, thus, the SecS protein has been completely predicted. There is a perfect alignment between whale and dolphin SPS1 proteins.

Finally, any SECIS element located in the 3’ UTR region has been found.

Taking into account these results we can conclude that the SPS1 of the whale, as in the human and the dolphin, is not a selenoprotein and it is part of the selenoproteins synthesis machinery.

SPS2

The SPS2 protein is found in the KI537994.1 scaffold of the whale’s genome between positions 4582956 and 4581670. The hit of the query sequence is in the negative strand. The gene encoding the protein contains 1 exon, but any intron. A single Sec residue was found.

Despite having compared this protein in both human and dolphin, the dolphin SecS sequence has higher similarity (98.6%) with the whale’s one. Therefore, the results shown previously correspond to the alignment with the dolphin protein. Even so, it is possible to conclude that the sequence of this protein is really similar in all the three species. In the whale, the first amino acid is a Met, thus, the SecS protein has been completely predicted.

Finally, an A grade SECIS element was found between positions 99434 and 99358, located in the 3’ UTR region.

Taking into account these results we can conclude that the SPS2 of the whale, as in the human and the dolphin, is a selenoprotein and it is part of the selenoproteins synthesis machinery.

Cys-homologues discussion

GPx5

The GPx5 protein is found in the KI537663.1 scaffold of the whale’s genome between positions 1185138 and 1185449. The hit of the query sequence is in the positive strand. The gene encoding the protein contains 5 introns and 6 exons. Any Sec residue was found in this gene.

Despite having compared this protein in both human and dolphin, the human GPx5 sequence is better annotated and starts by Met. Therefore, the results shown previously, correspond to the alingment with the human protein. Even so, it is possible to conclude that the sequence of this protein is really similar in all the three species. In the whale, the first amino acid is a Met, thus, the GPx5 protein has been completely predicted.
Finally, any SECIS element located in the 3’ UTR region has been found.

Taking into account these results we can conclude that the GPx5 of the whale, as in human and dolphin, is not a selenoprotein although it is part of the glutathione peroxidases family.

GPx7

The GPx7 protein is found in the KI537096.1 scaffold of the whale’s genome between positions 14602297 and 14601953. The hit of the query sequence is in the negative strand. The gene encoding the protein contains 3 introns and 4 exons. Any Sec residue was found in this gene.

Despite having compared this protein in both human and dolphin, the human GPx7 sequence is better annotated and starts by Met. Therefore, the results shown previously, correspond to the alingment with the human protein. Even so, it is possible to conclude that the sequence of this protein is really similar in all the three species. In the whale, the first amino acid is not a Met, thus, the GPx7 protein has not been completely predicted.

Finally, any SECIS element located in the 3’ UTR region has been found.

Taking into account these results we can conclude that the GPx7 of the whale, as in human and dolphin, is not a selenoprotein although it is part of the glutathione peroxidases family.

GPx8

The GPx8 protein is found in the KI538471.1 scaffold of the whale’s genome between positions 10619283 and 10619546. The hit of the query sequence is in the positive strand. The gene encoding the protein contains 2 introns and 3 exons. Any Sec residue was found in this gene.

Despite having compared this protein in both human and dolphin, the human GPx8 sequence is better annotated and starts by Met. Therefore, the results shown previously, correspond to the alingment with the human protein. Even so, it is possible to conclude that the sequence of this protein is really similar in all the three species. In the whale, the first amino acid is a Met, thus, the GPx8 protein has been completely predicted.

Finally, any SECIS element located in the 3’ UTR region has been found.

Taking into account these results we can conclude that the GPx8 of the whale, as in human and dolphin, is not a selenoprotein although it is part of the glutathione peroxidases family.

MrsA

The MsrA protein is found in the scaffold KI538342.1 of the whale’s genome between positions 8953841 and 8953677. The gene encoding the protein contains 10 introns and 11 exons. Any  Sec residue was found in this gene.

Despite having compared this protein with both human and dolphin, dolphin has a higher percentage of similarity (98.11%) with the minke whale. Therefore, the results shown previously correspond to the predicted protein MsrA of minke whale compared to the dolphin one. However, as is shown in T-coffee, the initial sequence alignment is not much correct, but the last amino acids are more conserved. In the whale, the first amino acid is not a Met, thus, the MsrA protein has not been completely predicted.

Finally, any SECIS element located in the 3’ UTR region has been found.

SelR3

The SelR3 protein is found in the scaffold KI537679.1 of the whale’s genome between positions 17725386 and 17725550. The hit of the query sequence is in the positive strand. The gene encoding the protein contains 9 introns and 10 exons. Any  Sec residue was found in this gene.

Despite having compared this protein with both human and dolphin, dolphin has a higher percentage of similarity (98.18%) with the minke whale. Therefore, the results shown previously correspond to the predicted protein SelR3 of minke whale compared to the dolphin one. However, as is shown in T-coffee, the initial sequence alignment is not much correct, but the last amino acids are more conserved. In the whale, the first amino acid is not a Met, thus, the SelR3 protein has not been completely predicted.

Finally, any SECIS element located in the 3’ UTR region has been found.

SelU1

The SelU1 protein is found in the scaffold KI537623.1 of the whale’s genome between positions 2174590 i 2174423. The hit of the query sequence is in the negative strand. The gene encoding the protein contains 4 introns and 5 exons. Any  Sec residue was found in this gene.

Despite having compared this protein with both human and dolphin, the human SelU1 sequence is better annotated and starts by Met. Therefore, the results shown previously, correspond to the alingment with the human protein. In the whale, the first amino acid is also a Met, thus, the SelU1 protein has been completely predicted.

Finally, any SECIS element located in the 3’ UTR region has been found.

SelU2

The SelU2 protein is found in the KI537598.1 scaffold of the whale’s genome between positions 31262201 and 31262031. The hit of the query sequence is in the negative strand. The gene encoding the protein contains 8 exons and 7 introns. Any Sec residue was found in this gene.

Despite having compared this protein in both human and dolphin, the human SelU2 sequence is better annotated and starts by Met.  Therefore, the results shown previously, correspond to the alignment with the human protein. The alignment between these two proteins is almost perfect, especially in the end of the sequence. However, in the whale, the first amino acid is not a Met; thus, the SelU2 protein has not been completely predicted.

Finally, no SECIS element was found in the 3’ UTR region of the gene described above.