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 act upstream of or within mitochondrial respirasome assembly and negative regulation of apoptotic process. Predicted to be located in membrane. Orthologous to human 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81710,026,961 - 10,027,885 (-)NCBIGRCr8
mRatBN7.21710,021,853 - 10,022,777 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1710,021,859 - 10,022,796 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1710,036,141 - 10,037,065 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01711,569,506 - 11,570,430 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01710,032,578 - 10,033,502 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01710,558,714 - 10,559,638 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1710,558,714 - 10,559,627 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01712,684,712 - 12,685,636 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41716,083,853 - 16,084,777 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1121,366,268 - 1,367,095 (+)NCBI
Celera1710,094,818 - 10,095,742 (-)NCBICelera
Cytogenetic Map17p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IEA)
mitochondrion  (IEA)

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  


Genomics

Comparative Map Data
Higd2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81710,026,961 - 10,027,885 (-)NCBIGRCr8
mRatBN7.21710,021,853 - 10,022,777 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1710,021,859 - 10,022,796 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1710,036,141 - 10,037,065 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01711,569,506 - 11,570,430 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01710,032,578 - 10,033,502 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01710,558,714 - 10,559,638 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1710,558,714 - 10,559,627 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01712,684,712 - 12,685,636 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41716,083,853 - 16,084,777 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1121,366,268 - 1,367,095 (+)NCBI
Celera1710,094,818 - 10,095,742 (-)NCBICelera
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 (+)EnsemblGRCh38hg38GRCh38
GRCh375175,815,752 - 175,816,762 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365175,748,390 - 175,749,357 (+)NCBINCBI36Build 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 Ensembl
GRCm381354,590,231 - 54,591,147 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1354,590,207 - 54,591,158 (+)EnsemblGRCm38mm10GRCm38
MGSCv371354,691,592 - 54,692,508 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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_Tasha
ROS_Cfam_1.0437,305,086 - 37,306,087 (-)NCBIROS_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_1.0
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
SpeTri2.0NW_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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473313,740,949 - 13,741,927 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Higd2a
5 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)17429913021293263Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17429913021293263Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
1581553Pur14Proteinuria QTL 145.30.0001urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17797996816317111Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17920136523653323Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17920136523653323Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17920136523653323Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17999128640540197Rat

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
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 3 43 54 39 14 39 8 11 74 35 41 11 8
Low 3 2 5 2
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000023515   ⟹   ENSRNOP00000023515
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
RefSeq 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
  ENSRNOT00000023515.7 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
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