SEPSECS (Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase) - Rat Genome Database

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Gene: SEPSECS (Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase) Canis lupus familiaris
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Symbol: SEPSECS
Name: Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase
RGD ID: 12109505
Description: ENCODES a protein that exhibits O-phosphoseryl-tRNA(Sec) selenium transferase activity (inferred); RNA binding (inferred); selenotransferase activity (inferred); INVOLVED IN conversion of seryl-tRNAsec to selenocys-tRNAsec (inferred); selenocysteine incorporation (inferred); translation (inferred); ASSOCIATED WITH cerebellar ataxia (ortholog); cerebellar hypoplasia (ortholog); genetic disease (ortholog); FOUND IN cytoplasm (inferred); nucleus (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC488852; O-phosphoseryl-tRNA(Sec) selenium transferase
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1385,071,011 - 85,106,272 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl385,069,742 - 85,102,347 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha387,581,301 - 87,617,670 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0386,042,457 - 86,079,026 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl386,042,315 - 86,079,014 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1385,175,693 - 85,212,054 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0385,280,327 - 85,316,666 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0385,666,236 - 85,702,832 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IEA)
nucleus  (IEA)

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
SEPSECS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1385,071,011 - 85,106,272 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl385,069,742 - 85,102,347 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha387,581,301 - 87,617,670 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0386,042,457 - 86,079,026 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl386,042,315 - 86,079,014 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1385,175,693 - 85,212,054 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0385,280,327 - 85,316,666 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0385,666,236 - 85,702,832 (+)NCBIUU_Cfam_GSD_1.0
SEPSECS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38425,120,014 - 25,160,582 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl425,120,014 - 25,160,550 (-)EnsemblGRCh38hg38GRCh38
GRCh37425,121,636 - 25,162,071 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36424,732,820 - 24,771,083 (-)NCBINCBI36Build 36hg18NCBI36
Celera425,570,424 - 25,611,003 (-)NCBICelera
Cytogenetic Map4p15.2NCBI
HuRef424,462,251 - 24,502,807 (-)NCBIHuRef
CHM1_1425,120,960 - 25,161,508 (-)NCBICHM1_1
T2T-CHM13v2.0425,101,930 - 25,142,501 (-)NCBIT2T-CHM13v2.0
Sepsecs
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39552,797,431 - 52,827,104 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl552,797,429 - 52,827,050 (-)EnsemblGRCm39 Ensembl
GRCm38552,640,089 - 52,669,764 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl552,640,087 - 52,669,708 (-)EnsemblGRCm38mm10GRCm38
MGSCv37553,034,646 - 53,060,940 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36552,931,655 - 52,957,949 (-)NCBIMGSCv36mm8
Celera550,018,495 - 50,044,811 (-)NCBICelera
Cytogenetic Map5C1NCBI
cM Map528.44NCBI
Sepsecs
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81462,524,287 - 62,554,529 (+)NCBIGRCr8
mRatBN7.21458,311,484 - 58,341,745 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1458,311,499 - 58,341,740 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1462,717,316 - 62,747,525 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01464,030,850 - 64,061,038 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01460,427,595 - 60,457,783 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01460,657,730 - 60,687,950 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1460,657,686 - 60,687,958 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01460,774,968 - 60,804,615 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1457,410,554 - 57,440,746 (+)NCBICelera
Cytogenetic Map14q11NCBI
Sepsecs
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544319,822,811 - 19,863,495 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544319,759,772 - 19,859,188 (+)NCBIChiLan1.0ChiLan1.0
SEPSECS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2325,366,640 - 25,407,835 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1425,557,647 - 25,601,542 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0419,517,552 - 19,558,454 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1424,802,260 - 24,842,816 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl424,802,260 - 24,842,816 (-)Ensemblpanpan1.1panPan2
Sepsecs
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528550,634,482 - 50,667,254 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364774,336,059 - 4,368,901 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364774,335,945 - 4,368,117 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEPSECS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl819,097,456 - 19,136,222 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1819,097,788 - 19,162,246 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2819,354,106 - 19,412,899 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SEPSECS
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12725,202,150 - 25,242,782 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2725,202,506 - 25,243,330 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604771,720,135 - 71,758,892 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sepsecs
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247557,211,584 - 7,250,748 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247557,211,598 - 7,250,748 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SEPSECS
506 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium 5 20 6 3 6 6 2 9 10 4
Low 5 2 3 4 3 8 2
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_014112655 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_014112656 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_014112657 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038472572 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038472573 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038482085 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038482096 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038533558 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038533559 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038597840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038597841 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038662062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038662063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSCAFT00000044428   ⟹   ENSCAFP00000036137
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl385,069,742 - 85,102,347 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845013314   ⟹   ENSCAFP00845010331
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl386,042,315 - 86,079,014 (+)Ensembl
RefSeq Acc Id: XM_038472572   ⟹   XP_038328500
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1385,175,695 - 85,212,054 (+)NCBI
RefSeq Acc Id: XM_038472573   ⟹   XP_038328501
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1385,175,693 - 85,212,054 (+)NCBI
RefSeq Acc Id: XM_038482085   ⟹   XP_038338013
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha387,581,304 - 87,617,670 (+)NCBI
RefSeq Acc Id: XM_038482096   ⟹   XP_038338024
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha387,581,301 - 87,617,670 (+)NCBI
RefSeq Acc Id: XM_038533558   ⟹   XP_038389486
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0385,666,239 - 85,702,832 (+)NCBI
RefSeq Acc Id: XM_038533559   ⟹   XP_038389487
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0385,666,236 - 85,702,832 (+)NCBI
RefSeq Acc Id: XM_038597840   ⟹   XP_038453768
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0385,280,330 - 85,316,666 (+)NCBI
RefSeq Acc Id: XM_038597841   ⟹   XP_038453769
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0385,280,327 - 85,316,666 (+)NCBI
RefSeq Acc Id: XM_038662062   ⟹   XP_038517990
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0386,042,460 - 86,079,026 (+)NCBI
RefSeq Acc Id: XM_038662063   ⟹   XP_038517991
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0386,042,457 - 86,079,026 (+)NCBI
RefSeq Acc Id: ENSCAFP00000036137   ⟸   ENSCAFT00000044428
RefSeq Acc Id: XP_038328501   ⟸   XM_038472573
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038328500   ⟸   XM_038472572
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038453769   ⟸   XM_038597841
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038453768   ⟸   XM_038597840
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038517991   ⟸   XM_038662063
- Peptide Label: isoform X2
- UniProtKB: A0A8C0LU29 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038517990   ⟸   XM_038662062
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LNY6 (UniProtKB/TrEMBL),   A0A8C0PV25 (UniProtKB/TrEMBL),   A0A8C0LU29 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038338024   ⟸   XM_038482096
- Peptide Label: isoform X2
- UniProtKB: A0A8C0LU29 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038338013   ⟸   XM_038482085
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LNY6 (UniProtKB/TrEMBL),   A0A8C0PV25 (UniProtKB/TrEMBL),   A0A8C0LU29 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038389487   ⟸   XM_038533559
- Peptide Label: isoform X2
- UniProtKB: A0A8C0LU29 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038389486   ⟸   XM_038533558
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LNY6 (UniProtKB/TrEMBL),   A0A8C0LU29 (UniProtKB/TrEMBL),   A0A8C0PV25 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845010331   ⟸   ENSCAFT00845013314

Promoters
RGD ID:13682841
Promoter ID:EPDNEW_C910
Type:initiation region
Name:SEPSECS_1
Description:Sep (O-phosphoserine) tRNA:Sec tRNA synthase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1385,069,661 - 85,069,721EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000016468 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00040001639 UniProtKB/TrEMBL
  ENSCAFG00845007550 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000044428.3 UniProtKB/TrEMBL
  ENSCAFT00040003115.1 UniProtKB/TrEMBL
  ENSCAFT00845013314 ENTREZGENE
  ENSCAFT00845013314.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.640.10 UniProtKB/TrEMBL
InterPro PyrdxlP-dep_Trfase UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_major UniProtKB/TrEMBL
  Sec-tRNA_Se_transferase UniProtKB/TrEMBL
  SepSecS/SepCysS UniProtKB/TrEMBL
NCBI Gene LOC488852 ENTREZGENE
PANTHER O-PHOSPHOSERYL-TRNA(SEC) SELENIUM TRANSFERASE UniProtKB/TrEMBL
  PTHR12944 UniProtKB/TrEMBL
Pfam SepSecS UniProtKB/TrEMBL
PIRSF SepSecS UniProtKB/TrEMBL
Superfamily-SCOP SSF53383 UniProtKB/TrEMBL
UniProt A0A8C0LNY6 ENTREZGENE
  A0A8C0LU29 ENTREZGENE
  A0A8C0PV25 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3MVQ8_CANLF UniProtKB/TrEMBL
  A0A8P0NNB4_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:59025 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-09-12 SEPSECS  Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase  LOC488852  O-phosphoseryl-tRNA(Sec) selenium transferase  Symbol and/or name change 5135510 APPROVED