Socs5 (suppressor of cytokine signaling 5) - Rat Genome Database

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Gene: Socs5 (suppressor of cytokine signaling 5) Rattus norvegicus
Analyze
Symbol: Socs5
Name: suppressor of cytokine signaling 5
RGD ID: 1564914
Description: Predicted to enable 1-phosphatidylinositol-3-kinase regulator activity; epidermal growth factor receptor binding activity; and receptor tyrosine kinase binding activity. Predicted to be involved in several processes, including negative regulation of macromolecule metabolic process; phosphatidylinositol phosphate biosynthetic process; and regulation of T-helper cell differentiation. Predicted to act upstream of or within epidermal growth factor receptor signaling pathway. Predicted to be part of phosphatidylinositol 3-kinase complex. Orthologous to human SOCS5 (suppressor of cytokine signaling 5); PARTICIPATES IN interleukin-4 signaling pathway; Jak-Stat signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC500616; RGD1564914; similar to Suppressor of cytokine signaling 5
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
mRatBN7.267,481,039 - 7,512,644 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl67,481,095 - 7,514,834 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx67,762,496 - 7,793,102 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.068,071,907 - 8,102,513 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.067,599,021 - 7,629,627 (-)NCBIRnor_WKY
Rnor_6.0610,671,311 - 10,705,610 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl610,674,371 - 10,704,977 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0620,659,713 - 20,697,182 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4610,552,177 - 10,582,783 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera67,217,143 - 7,247,749 (-)NCBICelera
Cytogenetic Map6q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
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
6. Inhibitors of cytokine signal transduction. Wormald S and Hilton DJ, J Biol Chem 2004 Jan 9;279(2):821-4. Epub 2003 Nov 7.
Additional References at PubMed
PMID:12242343   PMID:15590694   PMID:15695332   PMID:17464217   PMID:19176113   PMID:24255059  


Genomics

Comparative Map Data
Socs5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.267,481,039 - 7,512,644 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl67,481,095 - 7,514,834 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx67,762,496 - 7,793,102 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.068,071,907 - 8,102,513 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.067,599,021 - 7,629,627 (-)NCBIRnor_WKY
Rnor_6.0610,671,311 - 10,705,610 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl610,674,371 - 10,704,977 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0620,659,713 - 20,697,182 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4610,552,177 - 10,582,783 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera67,217,143 - 7,247,749 (-)NCBICelera
Cytogenetic Map6q12NCBI
SOCS5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38246,698,937 - 46,763,129 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl246,698,952 - 46,780,245 (+)EnsemblGRCh38hg38GRCh38
GRCh37246,926,076 - 46,990,268 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36246,779,603 - 46,843,431 (+)NCBINCBI36Build 36hg18NCBI36
Build 34246,837,999 - 46,901,578NCBI
Celera246,764,784 - 46,828,608 (+)NCBICelera
Cytogenetic Map2p21NCBI
HuRef246,663,409 - 46,727,912 (+)NCBIHuRef
CHM1_1246,856,418 - 46,920,225 (+)NCBICHM1_1
T2T-CHM13v2.0246,703,485 - 46,767,961 (+)NCBIT2T-CHM13v2.0
Socs5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391787,414,707 - 87,445,153 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1787,415,107 - 87,445,267 (+)EnsemblGRCm39 Ensembl
GRCm381787,107,278 - 87,137,647 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1787,107,679 - 87,137,839 (+)EnsemblGRCm38mm10GRCm38
MGSCv371787,507,019 - 87,536,925 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361787,016,005 - 87,045,911 (+)NCBIMGSCv36mm8
Celera1791,484,878 - 91,514,794 (+)NCBICelera
Cytogenetic Map17E4NCBI
Socs5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544113,593,342 - 13,657,389 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544113,593,342 - 13,657,389 (+)NCBIChiLan1.0ChiLan1.0
SOCS5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan12A79,631,595 - 79,696,153 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A46,813,589 - 46,878,102 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A47,745,216 - 47,808,566 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A47,804,431 - 47,806,041 (+)Ensemblpanpan1.1panPan2
SOCS5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11048,916,446 - 48,977,183 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1048,972,842 - 48,974,452 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1048,769,314 - 48,830,770 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01049,786,401 - 49,847,931 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1049,786,357 - 49,845,694 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11049,494,260 - 49,555,954 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01049,784,343 - 49,845,789 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01049,967,638 - 50,029,159 (+)NCBIUU_Cfam_GSD_1.0
Socs5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629234,102,393 - 34,159,407 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365085,531,002 - 5,587,549 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365085,531,002 - 5,588,022 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOCS5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl393,783,964 - 93,925,863 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1393,777,402 - 93,925,859 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2399,869,650 - 99,940,636 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SOCS5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11460,330,192 - 60,335,477 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1460,431,401 - 60,433,011 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
ChlSab1.1 Ensembl1460,431,401 - 60,433,011 (-)NCBIChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604551,352,938 - 51,515,428 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Socs5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473828,150,664 - 28,216,389 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473828,150,004 - 28,217,850 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Socs5
105 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:324
Count of miRNA genes:178
Interacting mature miRNAs:239
Transcripts:ENSRNOT00000020337
Prediction methods: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
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6127574569Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6127574569Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6127574569Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6127574569Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6127574569Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6507449719988050Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat


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 40 22 6 19 6 74 35 41 11
Low 3 35 35 35 8 11 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020337   ⟹   ENSRNOP00000020346
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl67,481,672 - 7,512,277 (-)Ensembl
Rnor_6.0 Ensembl610,674,371 - 10,704,977 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094405   ⟹   ENSRNOP00000084063
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl67,481,340 - 7,511,781 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108488   ⟹   ENSRNOP00000087303
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl67,481,095 - 7,514,834 (-)Ensembl
RefSeq Acc Id: NM_001109274   ⟹   NP_001102744
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.267,481,672 - 7,512,277 (-)NCBI
Rnor_6.0610,674,371 - 10,704,977 (+)NCBI
Rnor_5.0620,659,713 - 20,697,182 (+)NCBI
RGSC_v3.4610,552,177 - 10,582,783 (+)RGD
Celera67,217,143 - 7,247,749 (-)RGD
Sequence:
RefSeq Acc Id: XM_006239718   ⟹   XP_006239780
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.267,481,039 - 7,512,644 (-)NCBI
Rnor_6.0610,671,311 - 10,705,610 (+)NCBI
Rnor_5.0620,659,713 - 20,697,182 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001102744 (Get FASTA)   NCBI Sequence Viewer  
  XP_006239780 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02651 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102744   ⟸   NM_001109274
- UniProtKB: D3ZUE4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239780   ⟸   XM_006239718
- Peptide Label: isoform X1
- UniProtKB: D3ZUE4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000020346   ⟸   ENSRNOT00000020337
RefSeq Acc Id: ENSRNOP00000084063   ⟸   ENSRNOT00000094405
RefSeq Acc Id: ENSRNOP00000087303   ⟸   ENSRNOT00000108488
Protein Domains
SH2   SOCS box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZUE4-F1-model_v2 AlphaFold D3ZUE4 1-536 view protein structure

Transcriptome

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

Promoters
RGD ID:13694391
Promoter ID:EPDNEW_R4916
Type:multiple initiation site
Name:Socs5_1
Description:suppressor of cytokine signaling 5
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_6.0610,674,364 - 10,674,424EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564914 AgrOrtholog
BioCyc Gene G2FUF-38714 BioCyc
Ensembl Genes ENSRNOG00000028504 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020346 ENTREZGENE
  ENSRNOP00000020346.3 UniProtKB/TrEMBL
  ENSRNOP00000084063.1 UniProtKB/TrEMBL
  ENSRNOP00000087303 ENTREZGENE
  ENSRNOP00000087303.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020337 ENTREZGENE
  ENSRNOT00000020337.5 UniProtKB/TrEMBL
  ENSRNOT00000094405.1 UniProtKB/TrEMBL
  ENSRNOT00000108488 ENTREZGENE
  ENSRNOT00000108488.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.505.10 UniProtKB/TrEMBL
InterPro SH2 UniProtKB/TrEMBL
  SH2_dom_sf UniProtKB/TrEMBL
  SOCS UniProtKB/TrEMBL
  SOCS5_SOCS UniProtKB/TrEMBL
  SOCS_box_dom_like UniProtKB/TrEMBL
  SOCS_C UniProtKB/TrEMBL
KEGG Report rno:500616 UniProtKB/TrEMBL
NCBI Gene 500616 ENTREZGENE
PANTHER PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT UniProtKB/TrEMBL
  PTHR10155:SF15 UniProtKB/TrEMBL
Pfam SH2 UniProtKB/TrEMBL
  SOCS UniProtKB/TrEMBL
  SOCS_box UniProtKB/TrEMBL
PhenoGen Socs5 PhenoGen
PROSITE SH2 UniProtKB/TrEMBL
  SOCS UniProtKB/TrEMBL
SMART SH2 UniProtKB/TrEMBL
  SOCS UniProtKB/TrEMBL
  SOCS_box UniProtKB/TrEMBL
Superfamily-SCOP SSF158235 UniProtKB/TrEMBL
  SSF55550 UniProtKB/TrEMBL
UniProt D3ZUE4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Socs5  suppressor of cytokine signaling 5  RGD1564914_predicted  similar to Suppressor of cytokine signaling 5 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564914_predicted  similar to Suppressor of cytokine signaling 5 (predicted)  LOC500616  similar to Suppressor of cytokine signaling 5  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500616  similar to Suppressor of cytokine signaling 5      Symbol and Name status set to provisional 70820 PROVISIONAL