Sh2d1b (SH2 domain containing 1B) - Rat Genome Database

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Gene: Sh2d1b (SH2 domain containing 1B) Rattus norvegicus
Analyze
Symbol: Sh2d1b
Name: SH2 domain containing 1B
RGD ID: 1563935
Description: Orthologous to human SH2D1B (SH2 domain containing 1B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; thioacetamide.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC100910879; LOC501869; RGD1563935; SH2 domain protein 1B1; SH2 domain-containing protein 1B; SH2 domain-containing protein 1B-like; Sh2d1b1; similar to EWS/FLI1 activated transcript 2
RGD Orthologs
Human
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
GRCr81385,018,078 - 85,056,263 (+)NCBIGRCr8
mRatBN7.21382,485,076 - 82,519,401 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.01388,605,339 - 88,623,787 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1388,606,894 - 88,622,788 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01393,231,267 - 93,249,713 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41386,096,465 - 86,126,881 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1382,145,505 - 82,177,125 (+)NCBICelera
Cytogenetic Map13q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Biological Process

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
2. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:16920955   PMID:21873635  


Genomics

Comparative Map Data
Sh2d1b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81385,018,078 - 85,056,263 (+)NCBIGRCr8
mRatBN7.21382,485,076 - 82,519,401 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.01388,605,339 - 88,623,787 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1388,606,894 - 88,622,788 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01393,231,267 - 93,249,713 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41386,096,465 - 86,126,881 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1382,145,505 - 82,177,125 (+)NCBICelera
Cytogenetic Map13q24NCBI
SH2D1B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381162,395,268 - 162,412,136 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1162,395,268 - 162,412,138 (-)EnsemblGRCh38hg38GRCh38
GRCh371162,365,058 - 162,381,926 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361160,631,680 - 160,648,552 (-)NCBINCBI36Build 36hg18NCBI36
Celera1135,468,132 - 135,485,005 (-)NCBICelera
Cytogenetic Map1q23.3NCBI
HuRef1133,609,775 - 133,626,695 (-)NCBIHuRef
CHM1_11163,786,752 - 163,803,594 (-)NCBICHM1_1
T2T-CHM13v2.01161,739,274 - 161,756,137 (-)NCBIT2T-CHM13v2.0
Sh2d1b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546213,909,258 - 13,931,526 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546213,909,266 - 13,934,239 (+)NCBIChiLan1.0ChiLan1.0
SH2D1B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2187,372,995 - 87,390,617 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1187,041,163 - 87,058,755 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01137,809,079 - 137,836,330 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11141,606,641 - 141,623,436 (-)NCBIpanpan1.1PanPan1.1panPan2
SH2D1B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13820,303,987 - 20,326,065 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3820,303,709 - 20,321,761 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3820,359,190 - 20,381,832 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03820,388,245 - 20,410,691 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3820,388,278 - 20,410,903 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13820,362,264 - 20,385,003 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03820,715,280 - 20,737,939 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03821,005,937 - 21,026,009 (+)NCBIUU_Cfam_GSD_1.0
Sh2d1b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244050588,284,353 - 8,319,648 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004936831604,308 - 635,459 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SH2D1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1488,097,534 - 88,129,792 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2495,920,518 - 95,926,267 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SH2D1B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1201,667,247 - 1,684,951 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl201,668,588 - 1,682,949 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666038696,149 - 712,633 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sh2d1b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247879,077,658 - 9,078,053 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sh2d1b
227 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:76
Interacting mature miRNAs:79
Transcripts:ENSRNOT00000048692
Prediction methods:Microtar, Miranda, Rnahybrid
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
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
12879444Bp397Blood pressure QTL 397arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134504940490049404Rat
12879471Bp398Blood pressure QTL 398arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134551471990514719Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134619797684753113Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)135987440885581182Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)136906051986800898Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)136906051986800898Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)136906051986800898Rat
8655959Pur32Proteinuria QTL 328.4urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)137486211785581182Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat

Markers in Region
AU048833  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21382,507,205 - 82,507,359 (+)MAPPERmRatBN7.2
Rnor_6.01387,433,876 - 87,434,029NCBIRnor6.0
Rnor_5.01392,065,745 - 92,065,898UniSTSRnor5.0
RGSC_v3.41386,116,713 - 86,116,866UniSTSRGSC3.4
Celera1382,165,800 - 82,165,953UniSTS
Cytogenetic Map13q24UniSTS


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
Low 2 15 1 19 1 30 10 10 11
Below cutoff 1 36 39 37 37 2 4 40 23 24 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000048692   ⟹   ENSRNOP00000047078
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1388,606,894 - 88,622,788 (+)Ensembl
RefSeq Acc Id: XM_577285   ⟹   XP_577285
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81385,018,078 - 85,056,263 (+)NCBI
mRatBN7.21382,485,328 - 82,519,401 (+)NCBI
Rnor_6.01388,605,339 - 88,623,787 (+)NCBI
Rnor_5.01393,231,267 - 93,249,713 (+)NCBI
RGSC_v3.41386,096,465 - 86,126,881 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_577285 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM09254 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_577285   ⟸   XM_577285
- UniProtKB: D4A9E3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000047078   ⟸   ENSRNOT00000048692

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A9E3-F1-model_v2 AlphaFold D4A9E3 1-132 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:1563935 AgrOrtholog
BioCyc Gene G2FUF-17480 BioCyc
Ensembl Genes ENSRNOG00000031599 Ensembl
NCBI Gene 501869 ENTREZGENE
PhenoGen Sh2d1b PhenoGen
RatGTEx ENSRNOG00000031599 RatGTEx
UniProt D4A9E3 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Sh2d1b  SH2 domain containing 1B  LOC100910879  SH2 domain-containing protein 1B-like  Data merged from RGD:6496004 737654 PROVISIONAL
2012-07-05 LOC100910879  SH2 domain-containing protein 1B-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-25 Sh2d1b  SH2 domain containing 1B  Sh2d1b1  SH2 domain protein 1B1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-08-14 Sh2d1b1  SH2 domain protein 1B1  Sh2d1b  SH2 domain containing 1B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-04 Sh2d1b  SH2 domain containing 1B  Sh2d1b1  SH2 domain protein 1B1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Sh2d1b1  SH2 domain protein 1B1  RGD1563935_predicted  similar to EWS/FLI1 activated transcript 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1563935_predicted  similar to EWS/FLI1 activated transcript 2 (predicted)  LOC501869  similar to EWS/FLI1 activated transcript 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501869  similar to EWS/FLI1 activated transcript 2      Symbol and Name status set to provisional 70820 PROVISIONAL