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

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Gene: Sh2d1a (SH2 domain containing 1A) Rattus norvegicus
Analyze
Symbol: Sh2d1a
Name: SH2 domain containing 1A
RGD ID: 1562408
Description: Predicted to be involved in negative regulation of T cell receptor signaling pathway. Predicted to act upstream of or within humoral immune response 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: PROVISIONAL
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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X126,239,191 - 126,267,425 (+)NCBIGRCr8
mRatBN7.2X121,373,693 - 121,401,923 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_UtxX123,494,712 - 123,522,963 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X127,016,060 - 127,044,297 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X124,599,290 - 124,613,139 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X128,897,053 - 128,925,408 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX128,897,181 - 128,925,407 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X128,978,818 - 129,007,045 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X2,532,295 - 2,560,524 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX120,486,695 - 120,514,918 (+)NCBICelera
Cytogenetic MapXq35NCBI
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
cytoplasm  (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 (+)NCBIGRCr8
mRatBN7.2X121,373,693 - 121,401,923 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_UtxX123,494,712 - 123,522,963 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X127,016,060 - 127,044,297 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X124,599,290 - 124,613,139 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X128,897,053 - 128,925,408 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX128,897,181 - 128,925,407 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X128,978,818 - 129,007,045 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X2,532,295 - 2,560,524 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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 (+)EnsemblGRCh38hg38GRCh38
GRCh37X123,480,413 - 123,507,010 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X123,307,831 - 123,334,686 (+)NCBINCBI36Build 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 Ensembl
GRCm38X42,502,565 - 42,522,097 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX42,502,453 - 42,529,330 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X39,855,785 - 39,875,252 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX81,806,674 - 81,829,216 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X97,524,200 - 97,546,969 (+)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247973,120,123 - 3,142,564 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sh2d1a
120 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX112934952138400867Rat
5685004Bss104Bone structure and strength QTL 1043.9tibia area (VT:1000281)tibia area measurement (CMO:0001382)X113805422126975220Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat

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
RGSC_v3.1X2,558,881 - 2,559,044RGD
CeleraX120,488,175 - 120,488,337UniSTS
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
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 8 18 11 2
Low 2 11 16 8 1 8 1 1 12 4 9 9 1
Below cutoff 1 10 11 11 11 7 7 34 23 25 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008444   ⟹   ENSRNOP00000008444
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX128,897,181 - 128,925,407 (+)Ensembl
RefSeq Acc Id: NM_001109313   ⟹   NP_001102783
RefSeq Status: PROVISIONAL
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
Reference Protein Sequences
RefSeq Acc Id: NP_001102783   ⟸   NM_001109313
- UniProtKB: B2RZ59 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008444   ⟸   ENSRNOT00000008444
RefSeq Acc Id: XP_063136266   ⟸   XM_063280196
- Peptide Label: isoform X1
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
  ENSRNOG00055014907 UniProtKB/Swiss-Prot
  ENSRNOG00060021262 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00055025502 UniProtKB/Swiss-Prot
  ENSRNOT00060036851 UniProtKB/Swiss-Prot
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
  ENSRNOG00055014907 RatGTEx
  ENSRNOG00060021262 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