Higd2a (HIG1 hypoxia inducible domain family, member 2A) - Rat Genome Database

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Gene: Higd2a (HIG1 hypoxia inducible domain family, member 2A) Rattus norvegicus
Analyze
Symbol: Higd2a
Name: HIG1 hypoxia inducible domain family, member 2A
RGD ID: 1309691
Description: Predicted to be involved in mitochondrial respirasome assembly. Predicted to act upstream of or within negative regulation of apoptotic process and response to quercetin. Predicted to be located in mitochondrial membrane. Predicted to be active in mitochondrion and nucleus. Orthologous to several human genes including HIGD2A (HIG1 hypoxia inducible domain family member 2A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amphetamine; bis(2-ethylhexyl) phthalate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: HIG1 domain family member 2A, mitochondrial; HIG1 domain family, member 2A; LOC290999; RGD1309691; similar to RIKEN cDNA 2010110M21
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
GRCr81710,026,961 - 10,027,885 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1710,026,961 - 10,027,874 (-)EnsemblGRCr8
mRatBN7.21710,021,853 - 10,022,777 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1710,021,859 - 10,022,796 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1710,036,141 - 10,037,065 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01711,569,506 - 11,570,430 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01710,032,578 - 10,033,502 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01710,558,714 - 10,559,638 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1710,558,714 - 10,559,627 (-)Ensemblrn6Rnor6.0
Rnor_5.01712,684,712 - 12,685,636 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41716,083,853 - 16,084,777 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1710,094,818 - 10,095,742 (-)NCBICelera
RGSC_v3.1121,366,268 - 1,367,095 (+)NCBI
Cytogenetic Map17p14NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:18614015   PMID:21856340   PMID:22405070   PMID:34800366  


Genomics

Comparative Map Data
Higd2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81710,026,961 - 10,027,885 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1710,026,961 - 10,027,874 (-)EnsemblGRCr8
mRatBN7.21710,021,853 - 10,022,777 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1710,021,859 - 10,022,796 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1710,036,141 - 10,037,065 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01711,569,506 - 11,570,430 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01710,032,578 - 10,033,502 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01710,558,714 - 10,559,638 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1710,558,714 - 10,559,627 (-)Ensemblrn6Rnor6.0
Rnor_5.01712,684,712 - 12,685,636 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41716,083,853 - 16,084,777 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1710,094,818 - 10,095,742 (-)NCBICelera
RGSC_v3.1121,366,268 - 1,367,095 (+)NCBI
Cytogenetic Map17p14NCBI
HIGD2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385176,388,751 - 176,389,761 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5176,388,751 - 176,389,761 (+)Ensemblhg38GRCh38
GRCh375175,815,752 - 175,816,762 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365175,748,390 - 175,749,357 (+)NCBIBuild 36Build 36hg18NCBI36
Celera5172,685,350 - 172,686,317 (-)NCBICelera
Cytogenetic Map5q35.2NCBI
HuRef5170,740,347 - 170,741,314 (+)NCBIHuRef
CHM1_15175,248,732 - 175,249,699 (+)NCBICHM1_1
T2T-CHM13v2.05176,933,109 - 176,934,119 (+)NCBIT2T-CHM13v2.0
Higd2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391354,738,044 - 54,738,960 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1354,738,020 - 54,738,971 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381354,590,231 - 54,591,147 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1354,590,207 - 54,591,158 (+)Ensemblmm10GRCm38
MGSCv371354,691,592 - 54,692,508 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361354,599,853 - 54,600,769 (+)NCBIMGSCv36mm8
Celera1355,656,607 - 55,657,523 (+)NCBICelera
Cytogenetic Map13B1NCBI
cM Map1328.84NCBI
Higd2a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540828,689,781 - 28,690,762 (+)Ensembl
ChiLan1.0NW_00495540828,689,781 - 28,690,762 (+)NCBIChiLan1.0ChiLan1.0
HIGD2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24171,467,897 - 171,468,839 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15169,607,436 - 169,608,382 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05171,685,512 - 171,686,527 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15178,757,440 - 178,758,686 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5178,757,667 - 178,758,676 (+)EnsemblpanPan2panpan1.1
HIGD2A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1436,937,441 - 36,938,436 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha436,904,973 - 36,905,973 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0437,305,086 - 37,306,087 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl437,304,239 - 37,306,035 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1437,130,372 - 37,131,372 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0437,317,956 - 37,318,957 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0437,826,978 - 37,827,978 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Higd2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213121,636,820 - 121,638,117 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936597661,742 - 665,505 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936597661,740 - 662,752 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HIGD2A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl281,486,890 - 81,488,045 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1281,486,890 - 81,488,039 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2283,138,547 - 83,139,696 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HIGD2A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12378,392,364 - 78,393,407 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660759,521,048 - 9,522,056 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Higd2a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473313,740,949 - 13,741,915 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473313,740,949 - 13,741,927 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Higd2a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11472,931,717 - 72,932,668 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Higd2a
7 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:42
Count of miRNA genes:38
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000023515
Prediction methods: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
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17143999106Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17926675540968173Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17436005727233623Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17212084342054133Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17920650523859062Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17920650523859062Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)17622199858177198Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17920650523859062Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131706603Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17473353449733534Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17920650523859062Rat
1549900Iddm20Insulin dependent diabetes mellitus QTL 203.7pancreas integrity trait (VT:0010560)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)17122181410Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17136045694Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17121499218Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17473353449733534Rat
1581553Pur14Proteinuria QTL 145.30.0001urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17798524316523460Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17857434232199534Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17920650523859062Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17138037084Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17920650523859062Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17143999106Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17436005727233623Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17143999106Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17212084322087569Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17920650523859062Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17920650523859062Rat
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122877318Rat

Markers in Region
RH133064  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2122,777,024 - 2,777,234 (-)MAPPERmRatBN7.2
mRatBN7.21710,021,906 - 10,022,116 (+)MAPPERmRatBN7.2
Rnor_6.01710,558,768 - 10,558,977NCBIRnor6.0
Rnor_6.0124,546,604 - 4,546,813NCBIRnor6.0
Rnor_5.01712,684,766 - 12,684,975UniSTSRnor5.0
Rnor_5.0126,674,667 - 6,674,876UniSTSRnor5.0
RGSC_v3.41716,083,907 - 16,084,116UniSTSRGSC3.4
RGSC_v3.4121,366,613 - 1,366,822UniSTSRGSC3.4
Celera124,592,000 - 4,592,209UniSTS
Celera1710,094,872 - 10,095,081UniSTS
Cytogenetic Map12p12UniSTS
Cytogenetic Map17p14UniSTS


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
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000023515   ⟹   ENSRNOP00000023515
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1710,026,961 - 10,027,874 (-)Ensembl
mRatBN7.2 Ensembl1710,021,859 - 10,022,796 (-)Ensembl
Rnor_6.0 Ensembl1710,558,714 - 10,559,627 (-)Ensembl
RefSeq Acc Id: NM_001106102   ⟹   NP_001099572
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81710,026,961 - 10,027,885 (-)NCBI
mRatBN7.21710,021,853 - 10,022,777 (-)NCBI
Rnor_6.01710,558,714 - 10,559,638 (-)NCBI
Rnor_5.01712,684,712 - 12,685,636 (-)NCBI
RGSC_v3.41716,083,853 - 16,084,777 (-)RGD
Celera1710,094,818 - 10,095,742 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099572 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI66544 (Get FASTA)   NCBI Sequence Viewer  
  EDL94039 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000023515
  ENSRNOP00000023515.3
RefSeq Acc Id: NP_001099572   ⟸   NM_001106102
- UniProtKB: B2GV65 (UniProtKB/TrEMBL),   F7FGX2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000023515   ⟸   ENSRNOT00000023515
Protein Domains
HIG1

Transcriptome

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

Promoters
RGD ID:13700323
Promoter ID:EPDNEW_R10845
Type:multiple initiation site
Name:Higd2a_1
Description:HIG1 hypoxia inducible domain family, member 2A
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_6.01710,559,622 - 10,559,682EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309691 AgrOrtholog
BioCyc Gene G2FUF-10175 BioCyc
Ensembl Genes ENSRNOG00000017372 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023515 ENTREZGENE
  ENSRNOT00000023515.8 UniProtKB/TrEMBL
Gene3D-CATH 6.10.140.1320 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7301761 IMAGE-MGC_LOAD
InterPro Hypoxia_induced_prot_cons-reg UniProtKB/TrEMBL
  RCF1 UniProtKB/TrEMBL
KEGG Report rno:290999 UniProtKB/TrEMBL
MGC_CLONE MGC:188144 IMAGE-MGC_LOAD
NCBI Gene 290999 ENTREZGENE
PANTHER HIG1 DOMAIN FAMILY MEMBER 2A UniProtKB/TrEMBL
  HYPOXIA-INDUCBILE GENE 1 HIG1 -RELATED UniProtKB/TrEMBL
Pfam HIG_1_N UniProtKB/TrEMBL
PhenoGen Higd2a PhenoGen
PROSITE HIG1 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000017372 RatGTEx
UniProt B2GV65 ENTREZGENE, UniProtKB/TrEMBL
  F7FGX2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-05-18 Higd2a  HIG1 hypoxia inducible domain family, member 2A  Higd2a  HIG1 domain family, member 2A   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Higd2a  HIG1 domain family, member 2A   Higd2a_predicted  HIG1 domain family, member 2A (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Higd2a_predicted  HIG1 domain family, member 2A (predicted)  RGD1309691_predicted  similar to RIKEN cDNA 2010110M21 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1309691_predicted  similar to RIKEN cDNA 2010110M21 (predicted)  LOC290999_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC290999_predicted  similar to RIKEN cDNA 2010110M21 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL