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

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Sepsecs (Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase) Rattus norvegicus
Analyze
Symbol: Sepsecs
Name: Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase
RGD ID: 1589491
Description: Predicted to enable tRNA binding activity. Predicted to be involved in selenocysteine incorporation. Predicted to be located in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 2D. Orthologous to human SEPSECS (Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase); INTERACTS WITH acetamide; bisphenol A; gentamycin.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC679383; LOC679383; O-phosphoseryl-tRNA(Sec) selenium transferase; similar to DNA segment, Chr 5, ERATO Doi 135, expressed; uncharacterized protein LOC679383
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01464,030,850 - 64,061,038 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01460,427,595 - 60,457,783 (+)NCBIRnor_WKY
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (ISO)
nucleus  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:16230358  


Genomics

Comparative Map Data
Sepsecs
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01464,030,850 - 64,061,038 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01460,427,595 - 60,457,783 (+)NCBIRnor_WKY
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38425,120,014 - 25,160,582 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 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 - 25,142,372 (-)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
(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
PanPan1.1424,802,260 - 24,842,816 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl424,802,260 - 24,842,816 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0419,517,552 - 19,558,454 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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
(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 (+)EnsemblSpeTri2.0
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
58 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:455
Count of miRNA genes:238
Interacting mature miRNAs:303
Transcripts:ENSRNOT00000070892
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143999825175582726Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat

Markers in Region
BM386109  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21458,336,737 - 58,336,891 (+)MAPPERmRatBN7.2
Rnor_6.01460,682,952 - 60,683,104NCBIRnor6.0
Rnor_5.01460,799,617 - 60,799,769UniSTSRnor5.0
Celera1457,435,748 - 57,435,900UniSTS
RH 3.4 Map14486.48UniSTS
RH131015  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21458,341,402 - 58,341,592 (+)MAPPERmRatBN7.2
Rnor_6.01460,687,616 - 60,687,805NCBIRnor6.0
Rnor_5.01460,804,281 - 60,804,470UniSTSRnor5.0
Celera1457,440,412 - 57,440,601UniSTS


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 renal system reproductive system respiratory system appendage
High
Medium 3 4 56 41 19 41 1 1 68 35 41 11 1
Low 39 1 7 10 6 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000070892   ⟹   ENSRNOP00000065651
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1458,311,499 - 58,341,740 (+)Ensembl
Rnor_6.0 Ensembl1460,657,686 - 60,687,958 (+)Ensembl
RefSeq Acc Id: NM_001128287   ⟹   NP_001121759
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21458,311,544 - 58,341,737 (+)NCBI
Rnor_6.01460,657,730 - 60,687,950 (+)NCBI
Rnor_5.01460,774,968 - 60,804,615 (+)NCBI
Celera1457,410,554 - 57,440,746 (+)RGD
Sequence:
RefSeq Acc Id: XM_039092409   ⟹   XP_038948337
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21458,311,487 - 58,341,745 (+)NCBI
RefSeq Acc Id: XM_039092411   ⟹   XP_038948339
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21458,311,487 - 58,339,599 (+)NCBI
RefSeq Acc Id: XM_039092412   ⟹   XP_038948340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21458,312,203 - 58,341,745 (+)NCBI
RefSeq Acc Id: XR_005493009
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21458,311,484 - 58,325,451 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001121759 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948337 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948339 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948340 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI66584 (Get FASTA)   NCBI Sequence Viewer  
  EDL99886 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001121759   ⟸   NM_001128287
- UniProtKB: B2GV97 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000065651   ⟸   ENSRNOT00000070892
RefSeq Acc Id: XP_038948337   ⟸   XM_039092409
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948339   ⟸   XM_039092411
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038948340   ⟸   XM_039092412
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2GV97-F1-model_v2 AlphaFold B2GV97 1-504 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699334
Promoter ID:EPDNEW_R9859
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:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01460,657,722 - 60,657,782EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1589491 AgrOrtholog
BioCyc Gene G2FUF-15598 BioCyc
BioCyc Pathway PWY-6281 [L-selenocysteine biosynthesis II (archaea and eukaryotes)] BioCyc
Ensembl Genes ENSRNOG00000049244 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065651 ENTREZGENE
  ENSRNOP00000065651.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000070892 ENTREZGENE
  ENSRNOT00000070892.3 UniProtKB/TrEMBL
Gene3D-CATH 3.40.640.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7443474 IMAGE-MGC_LOAD
InterPro PyrdxlP-dep_Trfase_major_dom UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_major_sub1 UniProtKB/TrEMBL
  Sec-tRNA_Se_transferase UniProtKB/TrEMBL
  SLA/LP_auto_ag UniProtKB/TrEMBL
KEGG Report rno:679383 UniProtKB/TrEMBL
MGC_CLONE MGC:188321 IMAGE-MGC_LOAD
NCBI Gene 679383 ENTREZGENE
PANTHER Sec-tRNA_Se_transferase UniProtKB/TrEMBL
Pfam SLA_LP_auto_ag UniProtKB/TrEMBL
PhenoGen Sepsecs PhenoGen
PIRSF SepSecS UniProtKB/TrEMBL
Superfamily-SCOP PyrdxlP-dep_Trfase_major UniProtKB/TrEMBL
TIGRFAMs Selenium_SpcS UniProtKB/TrEMBL
UniProt B2GV97 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-09 Sepsecs  Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase  LOC679383  similar to DNA segment, Chr 5, ERATO Doi 135, expressed  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC679383  similar to DNA segment, Chr 5, ERATO Doi 135, expressed      Symbol and Name status set to provisional 70820 PROVISIONAL