Sh2d1a (SH2 domain containing 1A) - Rat Genome Database

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Gene: Sh2d1a (SH2 domain containing 1A) Rattus norvegicus
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Symbol: Sh2d1a
Name: SH2 domain containing 1A
RGD ID: 1562408
Description: Predicted to enable protein-macromolecule adaptor activity. Predicted to be involved in negative regulation of T cell receptor signaling pathway. Predicted to act upstream of or within humoral immune response; natural killer cell activation; and positive regulation of natural killer cell mediated cytotoxicity. Predicted to be located in cytoplasm. Human ortholog(s) of this gene implicated in X-linked lymphoproliferative syndrome 1. Orthologous to human SH2D1A (SH2 domain containing 1A); PARTICIPATES IN measles pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC501502; RGD1562408; SH2 domain protein 1A; SH2 domain-containing protein 1A; similar to SH2 domain protein 1A (Signaling lymphocyte activation molecule-associated protein); similar to SH2 domain protein 1A (Signaling lymphocyte activation molecule-associated protein) (SLAM-associated protein) (T c ell signal transduction molecule SAP)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X126,239,191 - 126,267,425 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX126,239,200 - 126,267,424 (+)EnsemblGRCr8
mRatBN7.2X121,373,693 - 121,401,923 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_UtxX123,494,712 - 123,522,963 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X127,016,060 - 127,044,297 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X124,599,290 - 124,613,139 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X128,897,053 - 128,925,408 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX128,897,181 - 128,925,407 (+)Ensemblrn6Rnor6.0
Rnor_5.0X128,978,818 - 129,007,045 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X2,532,295 - 2,560,524 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX120,486,695 - 120,514,918 (+)NCBICelera
Cytogenetic MapXq35NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,ISO)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG 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. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:9774102   PMID:12477932   PMID:12529646   PMID:16127454   PMID:16223723   PMID:19648922  


Genomics

Comparative Map Data
Sh2d1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X126,239,191 - 126,267,425 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX126,239,200 - 126,267,424 (+)EnsemblGRCr8
mRatBN7.2X121,373,693 - 121,401,923 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_UtxX123,494,712 - 123,522,963 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X127,016,060 - 127,044,297 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X124,599,290 - 124,613,139 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X128,897,053 - 128,925,408 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX128,897,181 - 128,925,407 (+)Ensemblrn6Rnor6.0
Rnor_5.0X128,978,818 - 129,007,045 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X2,532,295 - 2,560,524 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX120,486,695 - 120,514,918 (+)NCBICelera
Cytogenetic MapXq35NCBI
SH2D1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X124,346,563 - 124,373,160 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX124,227,868 - 124,373,197 (+)Ensemblhg38GRCh38
GRCh37X123,480,413 - 123,507,010 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X123,307,831 - 123,334,686 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34X123,205,728 - 123,232,540NCBI
CeleraX123,864,695 - 123,891,574 (+)NCBICelera
Cytogenetic MapXq25NCBI
HuRefX112,860,780 - 112,888,184 (+)NCBIHuRef
CHM1_1X123,391,547 - 123,418,040 (+)NCBICHM1_1
T2T-CHM13v2.0X122,657,134 - 122,683,529 (+)NCBIT2T-CHM13v2.0
Sh2d1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X41,591,442 - 41,610,974 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX41,591,330 - 41,618,207 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X42,502,565 - 42,522,097 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX42,502,453 - 42,529,330 (+)Ensemblmm10GRCm38
MGSCv37X39,855,785 - 39,875,252 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X38,747,235 - 38,766,702 (+)NCBIMGSCv36mm8
CeleraX30,076,629 - 30,095,977 (+)NCBICelera
Cytogenetic MapXA4NCBI
cM MapX23.2NCBI
Sh2d1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547310,346,943 - 10,370,575 (-)Ensembl
ChiLan1.0NW_00495547310,345,407 - 10,370,535 (-)NCBIChiLan1.0ChiLan1.0
SH2D1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X123,819,657 - 123,846,697 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X123,823,266 - 123,850,307 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X113,538,321 - 113,565,468 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X123,712,932 - 123,739,424 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX123,712,932 - 123,739,419 (+)EnsemblpanPan2panpan1.1
SH2D1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X95,739,568 - 95,762,117 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX95,739,669 - 95,760,698 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX81,806,674 - 81,829,216 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X97,524,200 - 97,546,969 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX97,524,314 - 97,546,969 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X94,955,406 - 94,977,948 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X96,711,780 - 96,734,289 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X96,501,732 - 96,524,277 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Sh2d1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X94,705,939 - 94,728,897 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364796,258,953 - 6,281,552 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364796,258,953 - 6,281,552 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SH2D1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX101,824,367 - 101,849,671 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X101,824,602 - 101,847,265 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X116,692,706 - 116,715,387 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SH2D1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366606537,084,938 - 37,111,292 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sh2d1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247973,120,123 - 3,142,564 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247973,120,123 - 3,142,564 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Sh2d1a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X109,359,640 - 109,380,822 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sh2d1a
105 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:156
Count of miRNA genes:113
Interacting mature miRNAs:136
Transcripts:ENSRNOT00000008444
Prediction methods:Miranda, Pita, Pita,Targetscan, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X120028026141353710Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X97528096142528096Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X120028026141353710Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX105359969157758123Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118973754157758123Rat
2302047Pia34Pristane induced arthritis QTL 345.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1996916163141916163Rat

Markers in Region
DXGot56  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X121,375,172 - 121,375,335 (+)MAPPERmRatBN7.2
Rnor_6.0X128,898,661 - 128,898,823NCBIRnor6.0
Rnor_5.0X128,980,298 - 128,980,460UniSTSRnor5.0
RGSC_v3.4X2,558,881 - 2,559,044RGDRGSC3.4
RGSC_v3.4X2,558,882 - 2,559,044UniSTSRGSC3.4
CeleraX120,488,175 - 120,488,337UniSTS
RGSC_v3.1X2,558,881 - 2,559,044RGD
RH 2.0 Map5738.3RGD
Cytogenetic MapXq11UniSTS
RH129944  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X121,394,412 - 121,394,569 (+)MAPPERmRatBN7.2
Rnor_6.0X128,917,900 - 128,918,056NCBIRnor6.0
Rnor_5.0X128,999,537 - 128,999,693UniSTSRnor5.0
RGSC_v3.4X2,539,650 - 2,539,806UniSTSRGSC3.4
CeleraX120,507,410 - 120,507,566UniSTS
RH 3.4 Map5717.1UniSTS
Cytogenetic MapXq11UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
14 9 38 115 67 66 35 92 35 6 284 158 9 88 69 72 31 1 1

Sequence


Ensembl Acc Id: ENSRNOT00000008444   ⟹   ENSRNOP00000008444
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX128,897,181 - 128,925,407 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000157081   ⟹   ENSRNOP00000098812
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX126,239,200 - 126,267,424 (+)Ensembl
RefSeq Acc Id: NM_001109313   ⟹   NP_001102783
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X126,239,200 - 126,267,425 (+)NCBI
mRatBN7.2X121,373,693 - 121,401,923 (+)NCBI
Rnor_6.0X128,897,181 - 128,925,408 (+)NCBI
Rnor_5.0X128,978,818 - 129,007,045 (+)NCBI
RGSC_v3.4X2,532,295 - 2,560,524 (-)RGD
CeleraX120,486,695 - 120,514,918 (+)RGD
Sequence:
RefSeq Acc Id: XM_063280196   ⟹   XP_063136266
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X126,239,191 - 126,260,104 (+)NCBI
RefSeq Acc Id: NP_001102783   ⟸   NM_001109313
- UniProtKB: B2RZ59 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000008444   ⟸   ENSRNOT00000008444
RefSeq Acc Id: XP_063136266   ⟸   XM_063280196
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000098812   ⟸   ENSRNOT00000157081
Protein Domains
SH2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2RZ59-F1-model_v2 AlphaFold B2RZ59 1-126 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562408 AgrOrtholog
BioCyc Gene G2FUF-1226 BioCyc
Ensembl Genes ENSRNOG00000006263 Ensembl
  ENSRNOG00000080232 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000157081 ENTREZGENE
Gene3D-CATH 3.30.505.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7389183 IMAGE-MGC_LOAD
InterPro SH2 UniProtKB/Swiss-Prot
  SH2_dom_sf UniProtKB/Swiss-Prot
  SH2_prot_1A UniProtKB/Swiss-Prot
  SH2D1A_SH2 UniProtKB/Swiss-Prot
KEGG Report rno:501502 UniProtKB/Swiss-Prot
MGC_CLONE MGC:189293 IMAGE-MGC_LOAD
NCBI Gene 501502 ENTREZGENE
PANTHER IPPC DOMAIN-CONTAINING PROTEIN UniProtKB/Swiss-Prot
  SH2 DOMAIN-CONTAINING PROTEIN UniProtKB/Swiss-Prot
Pfam SH2 UniProtKB/Swiss-Prot
PhenoGen Sh2d1a PhenoGen
PIRSF SH2_p1A UniProtKB/Swiss-Prot
PRINTS SH2DOMAIN UniProtKB/Swiss-Prot
PROSITE SH2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000006263 RatGTEx
  ENSRNOG00000080232 RatGTEx
SMART SH2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF55550 UniProtKB/Swiss-Prot
UniProt B2RZ59 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-01 Sh2d1a  SH2 domain containing 1A  Sh2d1a  SH2 domain protein 1A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Sh2d1a  SH2 domain protein 1A  RGD1562408_predicted  similar to SH2 domain protein 1A (Signaling lymphocyte activation molecule-associated protein) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-10 RGD1562408_predicted  similar to SH2 domain protein 1A (Signaling lymphocyte activation molecule-associated protein) (predicted)    similar to SH2 domain protein 1A (Signaling lymphocyte activation molecule-associated protein) (SLAM-associated protein) (T c ell signal transduction molecule SAP) (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1562408_predicted  similar to SH2 domain protein 1A (Signaling lymphocyte activation molecule-associated protein) (SLAM-associated protein) (T c ell signal transduction molecule SAP) (predicted)  LOC501502  similar to SH2 domain protein 1A (Signaling lymphocyte activation molecule-associated protein) (SLAM-associated protein) (T c ell signal transduction molecule SAP)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501502  similar to SH2 domain protein 1A (Signaling lymphocyte activation molecule-associated protein) (SLAM-associated protein) (T c ell signal transduction molecule SAP)      Symbol and Name status set to provisional 70820 PROVISIONAL