Hsh2d (hematopoietic SH2 domain containing) - Rat Genome Database

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Gene: Hsh2d (hematopoietic SH2 domain containing) Rattus norvegicus
Analyze
Symbol: Hsh2d
Name: hematopoietic SH2 domain containing
RGD ID: 2321939
Description: Predicted to enable protein-macromolecule adaptor activity. Predicted to act upstream of or within T cell activation; negative regulation of B cell apoptotic process; and negative regulation of mitochondrial depolarization. Predicted to be located in cytosol and mitochondrion. Predicted to be active in cytoplasm. Orthologous to human HSH2D (hematopoietic SH2 domain containing); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100360518; LOC306333; rCG38847-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81617,664,548 - 17,686,976 (-)NCBIGRCr8
mRatBN7.21617,630,519 - 17,649,932 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1617,635,322 - 17,647,991 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1617,694,901 - 17,707,608 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01618,827,024 - 18,839,690 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01617,747,830 - 17,760,538 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01619,336,400 - 19,349,868 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1619,336,271 - 19,349,080 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01619,194,746 - 19,207,770 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41618,060,515 - 18,072,470 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11618,060,512 - 18,068,141 (-)NCBI
Celera1617,849,742 - 17,862,624 (-)NCBICelera
Cytogenetic Map16p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)
cytosol  (IEA,ISO)
mitochondrion  (IEA,ISO)

Molecular Function

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12960172   PMID:15569688   PMID:15632090  


Genomics

Comparative Map Data
Hsh2d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81617,664,548 - 17,686,976 (-)NCBIGRCr8
mRatBN7.21617,630,519 - 17,649,932 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1617,635,322 - 17,647,991 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1617,694,901 - 17,707,608 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01618,827,024 - 18,839,690 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01617,747,830 - 17,760,538 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01619,336,400 - 19,349,868 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1619,336,271 - 19,349,080 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01619,194,746 - 19,207,770 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41618,060,515 - 18,072,470 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11618,060,512 - 18,068,141 (-)NCBI
Celera1617,849,742 - 17,862,624 (-)NCBICelera
Cytogenetic Map16p14NCBI
HSH2D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381916,134,028 - 16,158,575 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1916,134,028 - 16,158,575 (+)EnsemblGRCh38hg38GRCh38
GRCh371916,244,838 - 16,269,386 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361916,105,838 - 16,130,381 (+)NCBINCBI36Build 36hg18NCBI36
Build 341916,105,837 - 16,130,375NCBI
Celera1916,146,791 - 16,171,332 (+)NCBICelera
Cytogenetic Map19p13.11NCBI
HuRef1915,815,784 - 15,840,224 (+)NCBIHuRef
CHM1_11916,244,333 - 16,268,880 (+)NCBICHM1_1
T2T-CHM13v2.01916,268,094 - 16,292,640 (+)NCBIT2T-CHM13v2.0
Hsh2d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39872,943,512 - 72,954,802 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl872,943,482 - 72,955,371 (+)EnsemblGRCm39 Ensembl
GRCm38872,189,668 - 72,200,958 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl872,189,638 - 72,201,527 (+)EnsemblGRCm38mm10GRCm38
MGSCv37874,713,567 - 74,724,857 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36875,118,657 - 75,129,947 (+)NCBIMGSCv36mm8
Celera876,545,344 - 76,556,622 (+)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map834.87NCBI
Hsh2d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555241,393,325 - 1,397,490 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555241,392,805 - 1,399,662 (-)NCBIChiLan1.0ChiLan1.0
HSH2D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22021,011,827 - 21,025,070 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11920,017,614 - 20,030,717 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01915,629,688 - 15,643,636 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11916,611,480 - 16,624,500 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1916,611,500 - 16,624,500 (+)Ensemblpanpan1.1panPan2
HSH2D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12046,319,410 - 46,329,997 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2046,319,315 - 46,326,600 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2046,233,847 - 46,244,478 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02046,807,765 - 46,818,396 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2046,807,755 - 46,818,074 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12046,042,402 - 46,053,033 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02046,453,942 - 46,464,577 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02046,730,281 - 46,740,888 (-)NCBIUU_Cfam_GSD_1.0
Hsh2d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118204,821,311 - 204,827,851 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365964,371,480 - 4,376,985 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HSH2D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl261,418,055 - 61,427,144 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1261,418,042 - 61,430,795 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2261,050,327 - 61,056,981 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HSH2D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1614,644,424 - 14,660,859 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl614,649,814 - 14,660,089 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660744,832,539 - 4,848,876 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hsh2d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249081,108,552 - 1,116,615 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hsh2d
148 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:136
Count of miRNA genes:108
Interacting mature miRNAs:114
Transcripts:ENSRNOT00000038494
Prediction methods:Microtar, Miranda, 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
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
631517Scl9Serum cholesterol level QTL 93.3blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)161572643321034895Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16422773017696785Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat


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
nervous system
renal system
reproductive system
respiratory system
9 11 39 102 91 90 59 25 59 6 208 87 82 45 58 31

Sequence


Ensembl Acc Id: ENSRNOT00000038494   ⟹   ENSRNOP00000037214
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1617,635,322 - 17,647,991 (-)Ensembl
Rnor_6.0 Ensembl1619,336,271 - 19,349,080 (-)Ensembl
RefSeq Acc Id: NM_001271328   ⟹   NP_001258257
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81617,669,345 - 17,682,013 (-)NCBI
mRatBN7.21617,635,322 - 17,647,991 (-)NCBI
Rnor_6.01619,336,400 - 19,349,011 (-)NCBI
Rnor_5.01619,194,746 - 19,207,770 (-)NCBI
Celera1617,849,742 - 17,862,624 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006252795   ⟹   XP_006252857
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81617,669,355 - 17,686,967 (-)NCBI
mRatBN7.21617,634,684 - 17,649,929 (-)NCBI
Rnor_6.01619,336,400 - 19,349,868 (-)NCBI
Rnor_5.01619,194,746 - 19,207,770 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039094085   ⟹   XP_038950013
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81617,669,355 - 17,682,459 (-)NCBI
mRatBN7.21617,634,684 - 17,649,925 (-)NCBI
RefSeq Acc Id: XM_039094086   ⟹   XP_038950014
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81617,669,355 - 17,686,965 (-)NCBI
mRatBN7.21617,634,684 - 17,640,022 (-)NCBI
RefSeq Acc Id: XM_039094087   ⟹   XP_038950015
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81617,669,355 - 17,686,976 (-)NCBI
mRatBN7.21617,636,777 - 17,649,932 (-)NCBI
RefSeq Acc Id: XM_039094088   ⟹   XP_038950016
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81617,664,548 - 17,686,970 (-)NCBI
mRatBN7.21617,630,519 - 17,649,930 (-)NCBI
RefSeq Acc Id: XR_005494527
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81617,670,806 - 17,686,976 (-)NCBI
mRatBN7.21617,636,789 - 17,649,932 (-)NCBI
RefSeq Acc Id: NP_001258257   ⟸   NM_001271328
- UniProtKB: D3ZRF7 (UniProtKB/TrEMBL),   A6K9Q2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252857   ⟸   XM_006252795
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000037214   ⟸   ENSRNOT00000038494
RefSeq Acc Id: XP_038950016   ⟸   XM_039094088
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038950013   ⟸   XM_039094085
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038950014   ⟸   XM_039094086
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038950015   ⟸   XM_039094087
- Peptide Label: isoform X3
Protein Domains
SH2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZRF7-F1-model_v2 AlphaFold D3ZRF7 1-335 view protein structure

Transcriptome

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

Promoters
RGD ID:13699989
Promoter ID:EPDNEW_R10511
Type:single initiation site
Name:Hsh2d_1
Description:hematopoietic SH2 domain containing
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_6.01619,349,011 - 19,349,071EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2321939 AgrOrtholog
BioCyc Gene G2FUF-11875 BioCyc
Ensembl Genes ENSRNOG00000023614 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038494 ENTREZGENE
  ENSRNOT00000038494.6 UniProtKB/TrEMBL
Gene3D-CATH 3.30.505.10 UniProtKB/TrEMBL
InterPro SH2 UniProtKB/TrEMBL
  SH2_dom_sf UniProtKB/TrEMBL
KEGG Report rno:100360518 UniProtKB/TrEMBL
NCBI Gene 100360518 ENTREZGENE
PANTHER PTHR14388:SF3 UniProtKB/TrEMBL
  T CELL-SPECIFIC ADAPTER PROTEIN TSAD UniProtKB/TrEMBL
Pfam SH2 UniProtKB/TrEMBL
PhenoGen Hsh2d PhenoGen
PRINTS SH2DOMAIN UniProtKB/TrEMBL
PROSITE SH2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000023614 RatGTEx
SMART SH2 UniProtKB/TrEMBL
Superfamily-SCOP SSF55550 UniProtKB/TrEMBL
UniProt A6K9Q2 ENTREZGENE, UniProtKB/TrEMBL
  D3ZRF7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-07 LOC100360518  rCG38847-like  Hsh2d  hematopoietic SH2 domain containing  Data merged from RGD:1305696 737654 APPROVED
2012-08-07 Hsh2d  hematopoietic SH2 domain containing  LOC100360518  rCG38847-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100360518  rCG38847-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Hsh2d  hematopoietic SH2 domain containing   Hsh2d_predicted  hematopoietic SH2 domain containing (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Hsh2d_predicted  hematopoietic SH2 domain containing (predicted)      Symbol and Name status set to approved 70820 APPROVED