Ssr4 (signal sequence receptor subunit 4) - Rat Genome Database

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Gene: Ssr4 (signal sequence receptor subunit 4) Rattus norvegicus
Analyze
Symbol: Ssr4
Name: signal sequence receptor subunit 4
RGD ID: 62034
Description: Part of Sec61 translocon complex. Human ortholog(s) of this gene implicated in congenital disorder of glycosylation Iy. Orthologous to human SSR4 (signal sequence receptor subunit 4); PARTICIPATES IN Endoplasmic Reticulum-associated degradation pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: signal sequence receptor 4; signal sequence receptor delta; signal sequence receptor subunit delta; signal sequence receptor, delta; SSR-delta; translocon-associated protein subunit delta; TRAP-delta
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X156,675,658 - 156,679,545 (+)NCBIGRCr8
mRatBN7.2X151,524,191 - 151,528,218 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX151,524,009 - 151,528,202 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX153,665,496 - 153,669,368 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,228,726 - 157,232,598 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X154,900,550 - 154,904,422 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X156,995,763 - 156,999,702 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,995,779 - 156,999,650 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,743,829 - 152,747,782 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,710,430 - 159,714,302 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X159,785,864 - 159,789,736 (+)NCBI
Celera1136,361,467 - 136,365,339 (-)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. A tetrameric complex of membrane proteins in the endoplasmic reticulum. Hartmann E, etal., Eur J Biochem 1993 Jun 1;214(2):375-81.
4. KEGG: Kyoto Encyclopedia of Genes and Genomes KEGG
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
10. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
Additional References at PubMed
PMID:15489334   PMID:20458337   PMID:24625528  


Genomics

Comparative Map Data
Ssr4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X156,675,658 - 156,679,545 (+)NCBIGRCr8
mRatBN7.2X151,524,191 - 151,528,218 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX151,524,009 - 151,528,202 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX153,665,496 - 153,669,368 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,228,726 - 157,232,598 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X154,900,550 - 154,904,422 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X156,995,763 - 156,999,702 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,995,779 - 156,999,650 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,743,829 - 152,747,782 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,710,430 - 159,714,302 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X159,785,864 - 159,789,736 (+)NCBI
Celera1136,361,467 - 136,365,339 (-)NCBICelera
Cytogenetic MapXq37NCBI
SSR4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X153,794,159 - 153,798,512 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX153,793,516 - 153,798,499 (+)EnsemblGRCh38hg38GRCh38
GRCh37X153,059,614 - 153,063,967 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X152,713,288 - 152,717,148 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X152,580,940 - 152,584,800NCBI
CeleraX153,293,775 - 153,297,635 (+)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX141,716,658 - 141,720,995 (+)NCBIHuRef
CHM1_1X152,934,039 - 152,938,376 (+)NCBICHM1_1
T2T-CHM13v2.0X152,067,822 - 152,072,175 (+)NCBIT2T-CHM13v2.0
Ssr4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X72,830,778 - 72,834,432 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX72,830,634 - 72,834,436 (+)EnsemblGRCm39 Ensembl
GRCm38X73,787,023 - 73,790,828 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX73,787,028 - 73,790,830 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X71,032,367 - 71,036,167 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X70,039,782 - 70,043,542 (+)NCBIMGSCv36mm8
CeleraX65,039,301 - 65,043,101 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX37.41NCBI
Ssr4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955580507,672 - 511,498 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955580507,672 - 511,498 (+)NCBIChiLan1.0ChiLan1.0
SSR4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X153,835,008 - 153,839,247 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X153,838,724 - 153,842,858 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X143,344,286 - 143,349,272 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X153,230,137 - 153,235,124 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX153,230,137 - 153,235,124 (+)Ensemblpanpan1.1panPan2
SSR4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X121,608,802 - 121,613,796 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX121,608,944 - 121,613,795 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX106,938,106 - 106,942,847 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X124,750,416 - 124,755,158 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX124,750,416 - 124,755,158 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X120,519,688 - 120,524,430 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X123,034,686 - 123,039,427 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X122,796,880 - 122,801,622 (+)NCBIUU_Cfam_GSD_1.0
Ssr4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X118,937,689 - 118,941,483 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936809675,049 - 679,707 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936809675,178 - 679,245 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SSR4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX124,537,540 - 124,541,637 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X124,537,545 - 124,541,635 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X142,102,139 - 142,106,233 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SSR4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X128,221,671 - 128,225,628 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX128,221,443 - 128,225,873 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606566,089,006 - 66,092,962 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ssr4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624946472,339 - 475,989 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624946472,364 - 475,989 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ssr4
2 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:64
Count of miRNA genes:58
Interacting mature miRNAs:59
Transcripts:ENSRNOT00000064213
Prediction methods:Microtar, Rnahybrid, 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
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat

Markers in Region
RH127738  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,527,229 - 151,527,816 (-)MAPPERmRatBN7.2
Rnor_6.0X156,996,165 - 156,996,751NCBIRnor6.0
Rnor_5.01152,744,231 - 152,744,817UniSTSRnor5.0
RGSC_v3.4X159,713,329 - 159,713,915UniSTSRGSC3.4
Celera1136,361,854 - 136,362,440UniSTS
RH 3.4 Map11620.12UniSTS
Cytogenetic MapXq37UniSTS


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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000083557   ⟹   ENSRNOP00000070206
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,524,009 - 151,528,202 (+)Ensembl
Rnor_6.0 EnsemblX156,995,779 - 156,999,650 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107771   ⟹   ENSRNOP00000091397
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,524,668 - 151,528,202 (+)Ensembl
RefSeq Acc Id: NM_017199   ⟹   NP_058895
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,675,658 - 156,679,530 (+)NCBI
mRatBN7.2X151,524,331 - 151,528,203 (+)NCBI
Rnor_6.0X156,995,778 - 156,999,650 (-)NCBI
Rnor_5.01152,743,829 - 152,747,782 (-)NCBI
RGSC_v3.4X159,710,430 - 159,714,302 (+)RGD
Celera1136,361,467 - 136,365,339 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006229571   ⟹   XP_006229633
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,675,752 - 156,679,545 (+)NCBI
mRatBN7.2X151,524,191 - 151,528,218 (+)NCBI
Rnor_6.0X156,995,763 - 156,999,702 (-)NCBI
Rnor_5.01152,743,829 - 152,747,782 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063279850   ⟹   XP_063135920
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,675,749 - 156,679,545 (+)NCBI
RefSeq Acc Id: XM_063279851   ⟹   XP_063135921
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,675,752 - 156,679,545 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_058895   ⟸   NM_017199
- Peptide Label: precursor
- UniProtKB: Q07984 (UniProtKB/Swiss-Prot),   A6KRV0 (UniProtKB/TrEMBL),   A6KRU9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229633   ⟸   XM_006229571
- Peptide Label: isoform X1
- UniProtKB: A0A8L2R221 (UniProtKB/TrEMBL),   A6KRU9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070206   ⟸   ENSRNOT00000083557
RefSeq Acc Id: ENSRNOP00000091397   ⟸   ENSRNOT00000107771
RefSeq Acc Id: XP_063135920   ⟸   XM_063279850
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063135921   ⟸   XM_063279851
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q07984-F1-model_v2 AlphaFold Q07984 1-173 view protein structure

Transcriptome

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

Promoters
RGD ID:13702054
Promoter ID:EPDNEW_R12578
Type:initiation region
Name:Ssr4_1
Description:signal sequence receptor subunit 4
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_6.0X156,999,560 - 156,999,620EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:62034 AgrOrtholog
BioCyc Gene G2FUF-660 BioCyc
Ensembl Genes ENSRNOG00000053172 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000083557.2 UniProtKB/TrEMBL
  ENSRNOT00000107771.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6921620 IMAGE-MGC_LOAD
InterPro TRAP-delta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29435 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:72864 IMAGE-MGC_LOAD
NCBI Gene 29435 ENTREZGENE
PANTHER PTHR12731 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSLOCON-ASSOCIATED PROTEIN SUBUNIT DELTA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TRAP-delta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ssr4 PhenoGen
RatGTEx ENSRNOG00000053172 RatGTEx
TIGR TC228922
UniProt A0A8I6AFI7_RAT UniProtKB/TrEMBL
  A0A8L2R221 ENTREZGENE, UniProtKB/TrEMBL
  A6KRU9 ENTREZGENE, UniProtKB/TrEMBL
  A6KRV0 ENTREZGENE, UniProtKB/TrEMBL
  Q07984 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-11 Ssr4  signal sequence receptor subunit 4  Ssr4  signal sequence receptor, delta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-24 Ssr4  signal sequence receptor, delta  Ssr4  signal sequence receptor 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Ssr4  signal sequence receptor 4      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains predicted protein has a single transmembrane domain 61758