RESULTS

The following table shows, for each query the reference specie, the residue (U or C), its tblastn output, the scaffold selected, where is the gene located, the exonerate prediction for the protein,the Genewise prediction, the T-Coffee alignment for the best prediction (with both exonerate and Genewise) and the SECIS element prediction by Seblastian or/and SECISearch3. The legend used is shown below:




Selenoproteins - Selenoprotein Machinery

Selenoproteins

This table shows the presence of the genes encoding selenoproteins:

Protein
Reference species
Residue (U or C)
BLAST
Scaffold
Gene location (strand)
Gff
Tcoffee
Seblastian or SECISearch3
Exonerate
Genewise
Exonerate
Genewise
SECIS prediction
Protein Sequence
SECIS Image
Iodothyronine deiodinase (DIO)
DIO1
U
OMLM01002656.1
26008-27162 (-)
DIO2
U
OMLM01007644.1
54912-58034 (-)
DIO3a
U
OMLM01009181.1
18508-19299 (-)
DIO3b
U
OMLM01012438.1
77918-78655 (+)
Glutathione peroxidase (GPx)
GPx1a
U
OMLM01008245.1
30405-31613 (+)
GPx1b
U
OMLM01004028.1
115184-116333 (-)
GPx2
U
OMLM01020689.1
40818-41983 (-)
GPx3a
U
OMLM01011369.1
2388-3823 (-)
GPx3b
U
OMLM01006563.1
77562-78936 (-)
GPx4a
U
OMLM01007071.1
36543-37350 (+)
GPx4b
U
OMLM01021133.1
53146-55535 (-)
GPx7
C
OMLM01018267.1
14011-15778 (-)
GPx8
C
OMLM01014511.1
4706-6520 (+)
Methionine sulfoxide reductase A (MsrA)
MsrA_1
C
OMLM01000544.1
1461-21097 (+)
MsrA_2
C
OMLM01009250.1
119818-134704 (-)
Selenoprotein R (MSRB)
MSRB1a
U
OMLM01007873.1
24155-25304 (+)
MSRB1b
U
OMLM01020828.1
15774-16886 (+)
MSRB2
C
OMLM01005029.1
50653-53160 (+)
MSRB3
C
OMLM01009714.1
953-2615 (+)
15-kDa selenoprotein (Sel15)
Sel15
U
OMLM01002590.1
127859-132270 (+)
Fish selenoprotein 15 (SELENOE)
SELENOE
U
OMLM01000156.1
88242-90050 (+)
Selenoprotein H (SELENOH)
SELENOH
U
OMLM01018966.1
28565-30446 (-)
Selenoprotein I (SELENOI)
SELENOI
U
OMLM01006824.1
68289-75601 (-)
Selenoprotein J (SELENOJ1)
SELENOJ1
U
OMLM01009182.1
92932–95436 (-)
SELENOJ1.2
U
OMLM01014617.1
36606–42315 (-)
Selenoprotein K (SELENOK)
SELENOK
U
OMLM01000630.1
1212-2975 (+)
Selenoprotein L (SELENOL)
SELENOL
Selenoprotein M (SELENOM)
SELENOM
U
OMLM01020340.1
70537-73037 (+)
Selenoprotein N (SELENON)
SELENON
U
OMLM01014045.1
24931 - 29638 (-)
Selenoprotein O (SELENOO)
SELENOO1
U
OMLM01015002.1
32586 - 38561 (-)
SELENOO2
U
OMLM01014659.1.
12499-16682(+)
Selenoprotein P (SELENOP)
SELENOP_1
U
OMLM01003153.1
17918-20472 (-)
SELENOP_2
U(17)
OMLM01003444.1
7532-8721 (-)
U(16)
OMLM01003444.1
6998-8721 (-)
Selenoprotein S (SELENOS)
SELENOS
U
OMLM01015868.1
39217-43191 (-)
Selenoprotein T (SELENOT)
SELENOT1
U
OMLM01001838.1
89446-92565 (-)
SELENOT1b
U
OMLM01010512.1
10880-11374 (+)
SELENOT2
U
OMLM01010512.1
7482- 11565(+)
Selenoprotein U (SELENOU)
SELENOU1a
U
OMLM01011960.1
134886-135645 (+)
U
OMLM01011960.1
1988-4041 (+)
U
OMLM01011960.1
48147-49223 (+)
SELENOU2
C
OMLM01010914.1
122950-124461 (+)
SELENOU3
C
OMLM01010914.1
2614-5560(-)
Selenoprotein W (SELENOW)
SELENOW_1
U
OMLM01020360.1
63508-63826 (-)
SELENOW_2
U
SELENOW_3
U
OMLM01020360.1
63508-64058(-)
SELENOW
U
OMLM01020360.1
63285-63820 (-)
Selenophosphate synthetase (SEPHS)
SEPHS1
C
OMLM01014436.1
28334-32815 (-)
SEPHS2
U
OMLM01002683.1
73046-78070 (+)
Thioredoxin reductase (TXNRD)
TXNRD2
U
OMLM01003366.1
37010-53768 (-)
TXNRD3
U
OMLM01011900.1
58881-67244 (-)



Selenoproteins - Selenoprotein Machinery

Selenoprotein Machinery

This table shows the presence of the genes encoding selenoprotein machinery and selenium metabolism:

Protein
Reference species
Residue (U or C)
BLAST
Scaffold
Gene location (strand)
Gff
Tcoffee
Seblastian or SECISearch3
Exonerate
Genewise
Exonerate
Genewise
SECIS prediction
Protein Sequence
SECIS Image
Eukaryotic elongation factor (eEFsec)
eEFsec
C
OMLM01010753.1
13413-22703 (+)
Phosphoseryl-tRNA kinase (PSTK)
PSTK
C
OMLM01002072.1
67351-67494 (+)
C
OMLM01002072.1
67351-69442 (+)
SECIS binding protein 2 (SBP2)
SBP2_1
C
OMLM01005182.1
39571-42400 (-)
SBP2_2
C
OMLM01004801.1
109-28447 (-)
C
OMLM01004801.1
109-4962 (-)
C
OMLM01001115.1
49913-50470 (-)
tRNA Sec 1 associated protein 1 (SECp43)
SECp43_1
C
OMLM01001339.1
8057- 11136 (-)
SECp43_2
C
OMLM01008182.1
28375 - 35367 (+)
Selenocysteine synthase
SecS
C
OMLM01012508.1
13409-23568 (-)