SelR1b

SelR1b protein, in P. schlosseri, is codified by the contig KN481551.1, between the positions 2479 and 3411 of the positive strand. This protein has 6 exons:

• Exon 1: from position 2479 to position 2533.
• Exon 2: from position 3018 to position 3160.
• Exon 3: from position 3298 to position 3411. This exon contains an aligned selenocystein with the one found in zebrafish SelR1b protein.
• Exon 4: from position 4267 to position 4321.
• Exon 5: from position 4403 to position 4545.
• Exon 6: from position 4836 to position 4949.

A SECIS element and a selenoprotein were predicted by using Seblastian. The obtained selenoprotein had 3 exons and the U residue was in the number 3.

SelR2

SelR2 protein, in P. schlosseri, is codified by the contig KN475030.1, between the positions 22971 and 24766 of the positive strand. This protein has 5 exons:

• Exon 1: from position 22971 to position 23082.
• Exon 2: from position 23658 to position 23755.
• Exon 3: from position 24220 to position 24296.
• Exon 4: from position 24443 to position 24590.
• Exon 5: from position 24668 to position 24766.

SelR2 does not have any selenocysteine residue. However, this protein has 6 cysteine residues that are aligned with the ones found in the zebrafish SelR2 protein. After using Seblastian and SECISearch3, no results were obtained.

SelR3

SelR3 protein, in P. schlosseri, is codified by the contig JACM01052317.1, between the positions 809 and 3106 of the positive strand. This protein has 5 exons:

• Exon 1: from position 809 to position 921.
• Exon 2: from position 1030 to position 1107.
• Exon 3: from position 1182 to position 1210.
• Exon 4: from position 2482 to position 2579.
• Exon 5: from position 2990 to position 3106.

SelR3 does not have any selenocysteine residue. However, this protein has 5 cysteine residues that are aligned with the ones found in the zebrafish SelR3 protein. After using Seblastian and SECISearch3, no results were obtained.

SelS

P schlosseri SelS protein is codified by the contig KN472370.1, between positions 23645 and 30103 in the negative strand. It has 6 exons:

• Exon 1: from position 30070 to position 30103. This exon has a selenocysteine residue.
• Exon 2: from position 25593 to position 25727.
• Exon 3: from position 25408 to position 25514.
• Exon 4: from position 24486 to position 24581.
• Exon 5: from position 24327 to position 24393.
• Exon 6: from position 23645 to position 23721.

However, the sequence of zebrafish SelS protein does not contain any Sec residue but has aligned cysteine residues with P. schlosseri SelS. Seblastian did not provide any prediction. Nevertheless, by using SECISearch3, a SECIS element was found.

SelT1

This protein is encoded in the contig KN472607.1, between positions 224964 and 226784 in the negative strand. P. schlosseri SelT1 protein has 5 exons:

• Exon 1: from position 226654 to position 226784.
• Exon 2: from position 226043 to position 226153. This exon contains the selenocysteine residue of SelT1 protein.
• Exon 3: from position 225613 to position 225739.
• Exon 4: from position 225129 to position 225216.
• Exon 5: from position 224964 to position 225031.

A SECIS element and a selenoprotein were predicted by using Seblastian.

SelT1b

By using the methodology that has been described, no SelW1 could be predicted in P. schlosseri.

SelT2

This protein is codified in the contig KN472830.1, between positions 1757 and 4070 in the positive strand. In P. schlosseri, SelT2 has 5 exons:

• Exon 1: from position 1757 to position 1899.
• Exon 2: from position 1945 to position 1986.
• Exon 3: from position 2593 to position 2703. This exon contains the selenocysteine residue aligned with the one in zebrafish SelT2 protein.
• Exon 4: from position 3111 to position 3249.
• Exon 5: from position 3984 to position 4070.

After using Seblastian and SECISearch3, no results were obtained.

SelU1a(I)

To do the homology-based approach the zebrafish SelU1A protein could not be used because it was not starting with methionine (neither in SelenoDB or UniProt). This is the reason why the sequence from Homo sapiens, obtained from SelenoDB, was used to do the comparison. In this case, after using the methodology already described, two possible hits were obtained:SelU1A(I)

This protein of P. schlosseri is encoded by the contig KN484292.1, between the positions 53686 and 52121 in the positive strand. The structure of the protein is detailed below:

• Exon 1: from position 55965 to position 56121.
• Exon 2: from position 54947 to position 55038. There is a selenocysteine residue in this exon.
• Exon 3: from position 54738 to position 54878.
• Exon 4: from position 54079 to position 54243.
• Exon 5: from position 53686 to position 53766.
• Exon 6: from position 63059 to position 63233.
• Exon 7: from position 62533 to position 62624.
• Exon 8: from position 62320 to position 62460.
• Exon 9: from position 62072 to position 62236.
• Exon 10: from position 61919 to position 61999.

A SECIS element and a selenoprotein were predicted by using Seblastian. However, the obtained selenoprotein had 5 exons.

SelU1a(II)

SelU1A (II) protein is codified by the contig KN471901.1, between the positions 38923 and 42068 in the positive strand. It has 5 exons:

• Exon 1: from position 38923 to position 39067.
• Exon 2: from position 40010 to position 40101. This exon contains a Sec residue.
• Exon 3: from position 40660 to position 40800.
• Exon 4: from position 41751 to position 41915.
• Exon 5: from position 41988 to position 42068.

A SECIS element and a selenoprotein were predicted by using Seblastian.

SelU2

To do the homology-based approach the zebrafish SelU2 protein could not be used because it was not well annotated (neither in SelenoDB or UniProt). This is the reason why the sequence from Homo sapiens, obtained from SelenoDB, was used to do the comparison.

In P. schlosseri, the SelU2 protein is codified by the contig KN483383.1, between the positions 25145 and 35531 in the positive strand. It has 7 exons:

• Exon 1: from position 25145 to position 25193.
• Exon 2: from position 30913 to position 31031.
• Exon 3: from position 31195 to position 31263.
• Exon 4: from position 33175 to position 33228.
• Exon 5: from position 33320 to position 33425.
• Exon 6: from position 35186 to position 35320.
• Exon 7: from position 35404 to position 35531.

SelU2 protein does not contain any selenocysteine residue but it has 3 cysteine residues aligned with the same amino acid in the zebrafish protein. After using Seblastian and SECISearch3, no results were obtained.

SelU3

To do the homology-based approach the zebrafish SelU3 protein could not be used because it was not well annotated (neither in SelenoDB or UniProt). This is the reason why the sequence from Homo sapiens, obtained from SelenoDB, was used to do the comparison. SelU3 protein is codified by the contig KN479866.1, between positions 23728 and 64520 in the negative strand. It has 8 exons:

• Exon 1: from position 64439 to position 64520.
• Exon 2: from position 29869 to position 29933.
• Exon 3: from position 28911 to position 29115.
• Exon 4: from position 28434 to position 28485.
• Exon 5: from position 28289 to position 28352.
• Exon 6: from position 28068 to position 28143.
• Exon 7: from position 26946 to position 27064.
• Exon 8: from position 23728 to position 23742.

This protein has 3 cysteine residues aligned with the same amino acid in the zebrafish SelU3 protein. In addition, the P. schlosseri SelU3 protein has four Sec insertions among its sequence that are not found in the zebrafish one.

Seblastian did not provide any prediction. However, by using SECISearch3, a SECIS element was found.

SelW1

By using the methodology that has been described, no SelW1 could be predicted in P. schlosseri.

SelW2a

In P. schlosseri, SelW2a protein is encoded by the contig JACM01031559.1, between positions 123 and 2617 in the positive strand. This protein has 4 exons:

• Exon 1: from position 123 to position 151.
• Exon 2: from position 414 to position 511.
• Exon 3: from position 589 to position 665.
• Exon 4: from position 2537 to position 2617.

Seblastian did not provide any selenoprotein prediction. However, by using SECISearch3, a SECIS element was found.

SelW2b

SelW2b protein could not be predicted for P. schlosseri by following the detailed steps of this study.

TR2

To do the homology-based approach the zebrafish TR2 protein could not be used because it was not starting with methionine (neither in SelenoDB or UniProt). This is the reason why the sequence from Homo sapiens, obtained from SelenoDB, was used to do the comparison.

TR2 protein is codified by the contig KN477299.1 in P. schlosseri. However, it is not encoded by one gene only but two. The first gene is located between the positions 10548 and 67353, in the negative strand. It encodes 18 exons:

• Exon 1: from position 67338 to position 67353.
• Exon 2: from position 23009 to position 23074.
• Exon 3: from position 22876 to position 22932.
• Exon 4: from position 22644 to position 22788.
• Exon 5: from position 22412 to position 22486.
• Exon 6: from position 22207 to position 22285.
• Exon 7: from position 21994 to position 22056.
• Exon 8: from position 21796 to position 21866.
• Exon 9: from position 19465 to position 19484.
• Exon 10: from position 19258 to position 19349.
• Exon 11: from position 19002 to position 19176.
• Exon 12: from position 14078 to position 14214.
• Exon 13: from position 12202 to position 12297.
• Exon 14: from position 11940 to position 12032.
• Exon 15: from position 11040 to position 11111.
• Exon 16: from position 10748 to position 10845.
• Exon 17: from position 10548 to position 10674.
• Exon 18: from position 143715 to position 143777.

The second gene is located between the positions 12313 and 143777, also in the negative strand. It encodes for the las six exons of the TR2 protein:

• Exon 19: from position 135349 to position 135404.
• Exon 20: from position 67003 to position 67029.
• Exon 21: from position 64534 to position 64551.
• Exon 22: from position 60825 to position 60865 .
• Exon 23: from position 49221 to position 49228.
• Exon 24: from position 12313 to position 12357. This exon contains the selenocysteine residue.

Two SECIS elements were predicted by using SECISearch3. Nevertheless, Seblastian could not predict a selenoprotein because TR2 is encoded by two different contigs.

TR3

TR3 protein in P. schlosseri is encoded by two different contigs: KN483500.1 (between the positions 57978 and 61466, in the positive strand) and KN474115.1 (between positions 52548 and 55858, in the negative strand). The contig KN483500.1 encodes 10 exons of TR3:

• Exon 1: from position 57978 to position 58094.
• Exon 2: from position 58304 to position 58364.
• Exon 3: from position 58977 to position 59086.
• Exon 4: from position 59275 to position 59382.
• Exon 5: from position 59493 to position 59565.
• Exon 6: from position 59634 to position 59753.
• Exon 7: from position 59844 to position 59992.
• Exon 8: from position 60070 to position 60185.
• Exon 9: from position 60350 to position 60575.
• Exon 10: from position 61350 to position 61466.

The contig KN474115.1 encodes 6 exons of TR3:

• Exon 11: from position 55858 to position 55955.
• Exon 12: from position 54782 to position 54938.
• Exon 13: from position 54315 to position 54422.
• Exon 14: from position 53975 to position 54070.
• Exon 15: from position 53753 to position 53887.
• Exon 16: from position 52548 to position 52613. This exon contains the selenocysteine residue.

A SECIS element was predicted by using SECISearch3. Nevertheless, Seblastian could not predict a selenoprotein.

SecS

SecS protein is encoded in the contig KN484638.1, between positions 1409 and 12679, in the positive strand. The structure of the protein is detailed below:

• Exon 1: from position 1409 to position 1522.
• Exon 2: from position 1595 to position 1749.
• Exon 3: from position 3465 to position 3583.
• Exon 4: from position 3692 to position 3850.
• Exon 5: from position 4943 to position 5096.
• Exon 6: from position 5849 to position 5951.
• Exon 7: from position 6062 to position 6191.
• Exon 8: from position 7120 to position 7211.
• Exon 9: from position 9239 to position 9332.
• Exon 10: from position 10020 to position 10110.
• Exon 11: from position 12460 to position 12679.

It does not have any selenocysteine residue. However, this protein has 12 cysteine residues that are aligned with the ones found in the zebrafish SecS protein. After using Seblastian and SECISearch3, no results were obtained.

eEFsec

The protein eEFsec is located in the contig KN477770.1 between positions 77439 and 98118, in the positive strand. The gene codifies 7 exons:

• Exon 1: from position 77439 to position 77712.
• Exon 2: from position 80059 to position 80266.
• Exon 3: from position 81459 to position 81555.
• Exon 4: from position 82659 to position 82823.
• Exon 5: from position 84887 to position 85510.
• Exon 6: from position 91040 to position 91196.
• Exon 7: from position 97940 to position 98118.

eEFsec is not a selenoprotein: it does not contain any selenocysteine. For this reason, Seblastian could not predict a selenoprotein. However, SECISearch3 predicted a SECIS element.

PSTK

The protein PSTK of P. schlosseri is in the contig KN474861.1, between the positions 19572 and 21515, in the negative strand. It has 3 exons:

• Exon 1: from position 21369 to position 21515.
• Exon 2: from position 20490 to position 20733.
• Exon 3: from position 19572 to position 19708.

It does not contain any Sec residue and no SECIS element or Seblastian prediction could be obtained for PSTK. However, it has 5 cysteine residues that are aligned with the same amino acid in the zebrafish protein.

SBP2

This protein is codified by the contig KN472259.1, between positions 13351 and 23647 in the negative strand. SBP2 in P. schlosseri has 10 exons:

• Exon 1: from position 23404 to position 23647.
• Exon 2: from position 22966 to position 23001.
• Exon 3: from position 22551 to position 22703.
• Exon 4: from position 19525 to position 19776.
• Exon 5: from position 18333 to position 18448.
• Exon 6: from position 17203 to position 17313.
• Exon 7: from position 16195 to position16284.
• Exon 8: from position 15476 to position 15643.
• Exon 9: from position 14024 to position 14108.
• Exon 10: from position 13351 to position 13421.

SBP2 does not have any selenocysteine residue. However, this protein has 5 cysteine residues that are aligned with the ones found in the zebrafish SBP2 protein. Seblastian could not predict any selenocysteine but a SECIS element was obtained by SECISearch3.

SBP2L

To do the homology-based approach the zebrafish SBP2L protein could not be used because it was not well annotated (neither in SelenoDB or UniProt). This is the reason why the sequence from Homo sapiens, obtained from SelenoDB, was used to do the comparison.

SBP2L protein, in P. schlosseri, is codified by the contig KN470587.1, between the positions 4404 and 75221 of the positive strand. This protein has 12 exons:

• Exon 1: from position 4404 to position 4415.
• Exon 2: from position 7435 to position 7461.
• Exon 3: from position 52542 to position 52670.
• Exon 4: from position 52745 to position 52834.
• Exon 5: from position 53137 to position 53266.
• Exon 6: from position 53339 to position 53499.
• Exon 7: from position 53944 to position 54058.
• Exon 8: from position 54480 to position 54648.
• Exon 9: from position 54735 to position 54955.
• Exon 10: from position 55064 to position 55218.
• Exon 11: from position 55293 to position 55379.
• Exon 12: from position 75186 to position 75221.

SBP2L does not have any selenocysteine residue. However, this protein has 4 cysteine residues that are aligned with the ones found in the zebrafish SBP2L protein. After using Seblastian and SECISearch3, no results were obtained.

SPS

In P. schlosseri, SPS is aligned in the contig KN475839.1, between the positions 46190 and 48295, in the positive strand. This protein has 9 exons:

• Exon 1: from position 46190 to position 46285.
• Exon 2: from position 46363 to position 46459.
• Exon 3: from position 46811 to position 46914.
• Exon 4: from position 46981 to position 47088.
• Exon 5: from position 47163 to position 47317.
• Exon 6: from position 47411 to position 47501.
• Exon 7: from position 47591 to position 47690.
• Exon 8: from position 47766 to position 47978.
• Exon 9: from position 48084 to position 48295.

This protein does not include any selenocysteine residue but it has 9 cysteine residues well-aligned with the ones that are found in zebrafish SPS protein. A SECIS element was predicted by using SECISearch3. Nevertheless, Seblastian could not predict a selenoprotein.

SPS2

The protein SPS2 is codified by 2 different contigs: KN484547.1 (between the positions 11229 and 18200, in the positive strand) and KN469560.1 (between the positions 1277 and 20105, in the negative strand). The contig KN484547.1 encodes the first part of the protein:

• Exon 1: from position 11229 to position 11490, that contains the selenocysteine residue.
• Exon 2: from position 11841 to position 11864.
• Exon 3: from position 14667 to position 14776.
• Exon 4: from position 15689 to position 15796.
• Exon 5: from position 16369 to position 16523.
• Exon 6: from position 17005 to position 17095.
• Exon 7: from position 17315 to position 17414.
• Exon 8: from position 17986 to position 18200.

The contig KN469560.1 encodes the last part of the protein:

• Exon 9: from position 19928 to position 20105.
• Exon 10: from position 12772 to position 12800.

A SECIS element was predicted by using SECISearch3. However, Seblastian could not predict a selenoprotein.

Trnau1apa

Trnau1apa protein is encoded by the contig number KN468817.1, between the positions 40105 and 44000 from the negative strand. The predicted one has 6 exons:

• Exon 1: from position 43977 to position 44000.
• Exon 2: from position 43090 to position 43187.
• Exon 3: from position 42617 to position 42716.
• Exon 4: from position 41938 to position 41987.
• Exon 5: from position 40774 to position 40905.
• Exon 6: from position 40105 to position 40222.

It does not have any selenocysteine residue. However, this protein has 3 cysteine residues that are aligned with the ones found in the zebrafish Tranu1apa protein. After using Seblastian and SECISearch3, no results were obtained.

C2H6orf52

This protein is encoded by the contig number KN484243.1, between the positions 6525 and 9576 from the negative strand in P. schlosseri. The structure of is detailed below:

• Exon 1: from position 9541 to position 9576.
• Exon 2: from position 9286 to position 9383.
• Exon 3: from position 8731 to position 8830.
• Exon 4: from position 8042 to position 8094.
• Exon 5: from position 7848 to position 7976.
• Exon 6: from position 7368 to position 7484.
• Exon 7: from position 7163 to position 7294.
• Exon 8: from position 6976 to position 7084.
• Exon 9: from position 6842 to position 6884.
• Exon 10: from position 6525 to position 6640.

It does not contain any Sec residue and no SECIS element or Seblastian prediction could be obtained for this protein. However, it has 4 cysteine residues that are aligned with the same amino acid in the zebrafish protein.