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RESULTS
The results obtained are resumed in the table below which contains the selenoproteins, the cysteine homologues and the machinery proteins predicted in our analysis of the Pogona vitticeps selenoproteome.
For each protein we define in the columns 2 and 3 the scaffold and the gene location respectively. In the next columns we attach the relevant files which have been used in the protein prediction, which are: the results of tBLASTn, the exons of the proteins, the T-Coffees of the Exonerate and Genewise, the sequence of the SECIS selected, the Seblastian predicted protein and the SECIS structure.
In order to make our predictions we have used the the Anolis carolinensis and the Homo sapiens selenoproteomes, so we attach the files obtained from the A. carolinensis with a lizard image and the ones obtained from the human with a person image. Nevertheless, the black line in the images means that these documents could not be obtained or that they were not significant for the analysis, so they are not shown. The meaning of the different colours that have been used is:
|
 |
Found |
 |
Methionine problem |
 |
Not found |
 |
No hit |
 |
Found |
 |
Methionine problem |
 |
Not found |
 |
Not obtained |
SELENOPROTEINS AND CYSTEINE HOMOLOGUES
|
| Protein name |
Scaffold |
Gene location |
tBLASTn |
Exons |
Exonerate |
Genewise |
SECIS sequence |
Seblastian |
SECIS structure |
| Glutathione peroxidase (GPx) |
| GPx1 |
CEMB01545308.1 |
4557477-4560307 |
|
|
|
 |
|
|
|
| GPx2 |
CEMB01012720.1 |
1089793-1093950 |
|
|
|
 |
|
|
|
| GPx3 |
CEMB01545298.1 |
148704-230484 |
|
|
|
 |
|
|
|
| GPx4 |
CEMB01020348.1 |
449454-458335 |
|
|
|
|
|
|
|
| GPx5 |
CEMB01006746.1 |
201027-201269 |
|
|
|
|
|
|
|
| GPx6 |
CEMB01545308 |
4557477-4560307 |
|
|
|
 |
|
|
|
| GPx7 |
CEMB01025174.1 |
1189829-1249111 |
|
|
|
|
|
|
|
| GPx8 |
CEMB01025174.1 |
1189829-1196100 |
|
|
|
|
|
|
|
| Iodothyronine deiodinase (DI) |
| DI1 |
CEMB01015858.1 |
845129- 851790 |
|
|
|
|
|
|
|
| DI2 |
CEMB01024191.1 |
69236-86155 |
|
|
|
|
|
|
|
| DI3 |
CEMB01002674.1 |
1655498- 1656337 |
|
|
|
|
|
|
|
| Methionine sulfoxide reductase A (MsrA) |
| MsrA |
CEMB01004415.1 |
1787-119750 |
|
|
|
|
|
|
|
| Methionine-R-sulfoxide reductase (MSRB) |
| MSRB1 |
CEMB01034240.1 |
245530-325002 |
|
|
|
|
|
|
|
| MSRB2 |
CEMB01029512.1 |
6866660-6929453 |
|
|
|
|
|
|
|
| MSRB3 |
CEMB01015116.1 |
2239081-2312173 |
|
|
|
|
|
|
|
| 15KDa selenoprotein (Sel15) |
| Sel15 |
CEMB01029493.1 |
105905-155503 |
|
|
|
|
|
|
|
| Selenoprotein H (SelH) |
| SelH |
CEMB01002966.1 |
930352-933503 |
|
|
|
|
|
|
|
| Selenoprotein I (SelI) |
| SelI |
CMB01020366.1 |
114743-208479 |
|
|
|
|
|
|
|
| Selenoprotein K (SelK) |
| SelK |
CEMB01006654.1 |
1858186-1863288 |
|
|
|
|
|
|
|
| Selenoprotein M (SelM) |
| SelM |
CEMB01008420.1 |
92412- 162538 |
|
|
|
|
|
|
|
| Selenoprotein N (SelN) |
| SelN |
CEMB01037816.1 |
1211310-1227196 |
|
|
|
 |
|
|
|
| Selenoprotein O (SelO) |
| SelO |
CEMB01025919.1 |
171404-282103 |
|
|
|
|
|
|
|
| Selenoprotein P (SelP) |
| SelP |
CEMB01031586.1 |
3789864-3884508 |
|
|
|
|
|
|
|
| Methionine-R-sufoxide reductase (SelR) |
| SelR1 |
CEMB01034240.1 |
245530-325002 |
|
|
|
|
|
|
|
| SelR2 |
CEMB01029512.1 |
6866660-6929453 |
|
|
|
|
|
|
|
| SelR3 |
CEMB01015116.1 |
2239081-2340634 |
|
|
|
|
|
|
|
| Selenoprotein S (SelS) |
| SelS |
CMB01545307.1 |
2383099-2451895 |
|
|
|
|
|
|
|
| Selenoprotein T (SelT) |
| SelT |
CEMB01025449.1 |
2390177-2399217 |
|
|
|
|
|
|
|
| Selenoprotein U (SelU) |
| SelU1 |
CEMB01004403.1 |
1495870-1503336 |
|
|
|
|
|
|
|
| SelU2 |
CEMB01001592.1 |
719555-760989 |
|
|
|
|
|
|
|
| SelU3 |
CEMB01011587.1 |
566369-574331 |
|
|
|
|
|
|
|
| Selenoprotein V (SelV) |
| SelV |
- |
- |
|
|
|
|
|
|
|
| Selenoprotein W (SelW) |
| SelW1 |
CEMB01027437.1 |
18032-23866 |
|
|
|
|
|
|
|
| SelW2 |
CEMB01003800.1 |
1676926-1754339 |
|
|
|
|
|
|
|
| Thioredoxin reductase (TR) |
| TR1 |
CEMB01031819.1 |
1005603-1033533 |
|
|
|
|
|
|
|
| TR2 |
CEMB01011310.1 |
12980-33706 |
|
|
|
|
|
|
|
| TR3 |
CEMB01011310.1 |
7607-33706 |
|
|
|
|
|
|
|
MACHINERY
|
| Protein name |
Scaffold |
Gene location |
tBLASTn |
Exons |
Exonerate |
Genewise |
SECIS sequence |
Seblastian |
SECIS structure |
| Eukaryotic elongation factor (eEFsec) |
| eEFsec |
CEMB01008168.1 |
332147-553028 |
|
|
|
|
|
|
|
| Phosphoseryl-tRNA kinase (PSTK) |
| PSTK |
CEMB01002406.1 |
243615-348310 |
|
|
|
|
|
|
|
| SECIS binding protein 2 (SBP2) |
| SBP2 |
CEMB01007019.1 |
1606605-1648886 |
|
|
|
|
|
|
|
| tRNA Sec 1 associated protein 1 (SECp43) |
| Secp43 |
CEMB01011943.1 |
1979887-1991795 |
|
|
|
|
|
|
|
| Selenocysteine synthase (SecS) |
| SecS |
CEMB01019488.1 |
3072240-3123698 |
|
|
|
|
|
|
|
| Selenophosphate synthetase (SPS) |
| SEPHS1 |
CEMB01026985.1 |
17484-66734 |
|
|
|
|
|
|
|
| SPS2 |
CEMB01025354.1 |
287066-489263 |
|
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