Higd1a (HIG1 hypoxia inducible domain family, member 1A) - Rat Genome Database

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Gene: Higd1a (HIG1 hypoxia inducible domain family, member 1A) Rattus norvegicus
Analyze
Symbol: Higd1a
Name: HIG1 hypoxia inducible domain family, member 1A
RGD ID: 620215
Description: Predicted to be involved in several processes, including cellular response to glucose starvation; mitochondrial respirasome assembly; and negative regulation of release of cytochrome c from mitochondria. Predicted to localize to mitochondrial inner membrane; nucleoplasm; and protein-containing complex. Orthologous to human HIGD1A (HIG1 hypoxia inducible domain family member 1A); INTERACTS WITH 2,4-dinitrotoluene; 3,3',4,4',5-pentachlorobiphenyl; 3,3',5-triiodo-L-thyronine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Hig1; HIG1 domain family member 1A; HIG1 domain family member 1A, mitochondrial; HIG1 domain family, member 1A; Hig1-pending; hypoxia induced gene 1; hypoxia-inducible gene 1 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28121,514,152 - 121,523,382 (-)NCBI
Rnor_6.0 Ensembl8130,482,493 - 130,491,998 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08130,482,492 - 130,491,888 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08129,660,254 - 129,669,650 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48127,076,654 - 127,085,885 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18127,096,390 - 127,105,621 (+)NCBI
Celera8120,638,935 - 120,648,165 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-diaminotoluene  (ISO)
2,4-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5-triiodo-L-thyronine  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxyphenyl retinamide  (ISO)
aflatoxin B1  (ISO)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
clozapine  (ISO)
cobalt dichloride  (EXP)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
finasteride  (EXP)
fluoranthene  (ISO)
flutamide  (EXP)
glafenine  (EXP)
haloperidol  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methylmercury chloride  (ISO)
mifepristone  (ISO)
nefazodone  (EXP)
nickel dichloride  (EXP,ISO)
nimesulide  (EXP)
oxaliplatin  (EXP)
paracetamol  (ISO)
perfluorooctanoic acid  (EXP)
phenylephrine  (EXP)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
quercetin  (EXP)
rac-lactic acid  (ISO)
Soman  (EXP)
sulindac  (EXP)
tamoxifen  (ISO)
Tesaglitazar  (EXP)
tetrachloromethane  (ISO)
tolcapone  (EXP)
topotecan  (EXP)
triclosan  (ISO)
triptonide  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

References

Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:15968589   PMID:16815968   PMID:18614015   PMID:21856340   PMID:22350989   PMID:23646141   PMID:25683712   PMID:30302618  


Genomics

Comparative Map Data
Higd1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28121,514,152 - 121,523,382 (-)NCBI
Rnor_6.0 Ensembl8130,482,493 - 130,491,998 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08130,482,492 - 130,491,888 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08129,660,254 - 129,669,650 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48127,076,654 - 127,085,885 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18127,096,390 - 127,105,621 (+)NCBI
Celera8120,638,935 - 120,648,165 (-)NCBICelera
Cytogenetic Map8q32NCBI
HIGD1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl342,784,298 - 42,804,531 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl342,782,908 - 42,804,490 (-)EnsemblGRCh38hg38GRCh38
GRCh38342,782,908 - 42,804,490 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37342,824,400 - 42,845,982 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36342,799,404 - 42,821,031 (-)NCBINCBI36hg18NCBI36
Celera342,764,774 - 42,783,944 (-)NCBI
Cytogenetic Map3p22.1NCBI
HuRef342,870,039 - 42,889,209 (-)NCBIHuRef
CHM1_1342,775,554 - 42,796,009 (-)NCBICHM1_1
Higd1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399121,677,623 - 121,686,862 (-)NCBIGRCm39mm39
GRCm39 Ensembl9121,677,629 - 121,687,428 (-)Ensembl
GRCm389121,848,557 - 121,857,796 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9121,848,563 - 121,858,362 (-)EnsemblGRCm38mm10GRCm38
MGSCv379121,757,678 - 121,767,118 (-)NCBIGRCm37mm9NCBIm37
MGSCv369121,697,261 - 121,706,324 (-)NCBImm8
Celera9122,323,317 - 122,332,728 (-)NCBICelera
Cytogenetic Map9F4NCBI
Higd1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542028,045,410 - 28,049,758 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542028,040,320 - 28,050,723 (+)NCBIChiLan1.0ChiLan1.0
HIGD1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1343,754,154 - 43,773,553 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl343,754,154 - 43,773,460 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0342,692,771 - 42,710,654 (-)NCBIMhudiblu_PPA_v0panPan3
HIGD1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12311,893,117 - 11,903,934 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2311,869,318 - 11,878,310 (-)NCBI
ROS_Cfam_1.02312,184,523 - 12,193,595 (-)NCBI
UMICH_Zoey_3.12311,986,828 - 11,995,831 (-)NCBI
UNSW_CanFamBas_1.02312,129,102 - 12,138,150 (-)NCBI
UU_Cfam_GSD_1.02312,132,754 - 12,141,746 (-)NCBI
Higd1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118199,978,953 - 199,989,050 (+)NCBI
SpeTri2.0NW_0049366952,330,939 - 2,341,387 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HIGD1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1326,278,208 - 26,286,199 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11326,278,202 - 26,286,334 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21328,946,329 - 28,954,443 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HIGD1A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1224,239,323 - 4,255,547 (-)NCBI
Vero_WHO_p1.0NW_023666041162,946,069 - 162,961,671 (+)NCBI
Higd1a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473076,944,785 - 76,954,873 (+)NCBI

Position Markers
RH132084  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28121,514,180 - 121,514,330 (+)MAPPER
Rnor_6.08130,482,521 - 130,482,670NCBIRnor6.0
Rnor_5.08129,660,283 - 129,660,432UniSTSRnor5.0
RGSC_v3.48127,085,707 - 127,085,856UniSTSRGSC3.4
Celera8120,638,964 - 120,639,113UniSTS
RH 3.4 Map81255.9UniSTS
Cytogenetic Map8q32UniSTS
AW049839  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28121,518,616 - 121,518,702 (+)MAPPER
mRatBN7.2X68,228,991 - 68,229,077 (+)MAPPER
Rnor_6.0X74,057,679 - 74,057,764NCBIRnor6.0
Rnor_6.08130,486,957 - 130,487,042NCBIRnor6.0
Rnor_5.08129,664,719 - 129,664,804UniSTSRnor5.0
Rnor_5.0X74,862,526 - 74,862,611UniSTSRnor5.0
RGSC_v3.4X91,184,148 - 91,184,233UniSTSRGSC3.4
RGSC_v3.48127,081,334 - 127,081,419UniSTSRGSC3.4
Celera8120,643,400 - 120,643,485UniSTS
CeleraX69,597,281 - 69,597,366UniSTS
Cytogenetic Map8q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)889058229132243842Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8104682575133307652Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:153
Count of miRNA genes:118
Interacting mature miRNAs:137
Transcripts:ENSRNOT00000064114
Prediction methods:Miranda, 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.


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 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000064114   ⟹   ENSRNOP00000061362
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8130,482,493 - 130,491,998 (-)Ensembl
RefSeq Acc Id: NM_080902   ⟹   NP_543178
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28121,514,152 - 121,523,382 (-)NCBI
Rnor_6.08130,482,492 - 130,491,888 (-)NCBI
Rnor_5.08129,660,254 - 129,669,650 (-)NCBI
RGSC_v3.48127,076,654 - 127,085,885 (+)RGD
Celera8120,638,935 - 120,648,165 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_543178 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH59118 (Get FASTA)   NCBI Sequence Viewer  
  AAL38979 (Get FASTA)   NCBI Sequence Viewer  
  EDL76814 (Get FASTA)   NCBI Sequence Viewer  
  Q8VH49 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_543178   ⟸   NM_080902
- UniProtKB: Q8VH49 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000061362   ⟸   ENSRNOT00000064114
Protein Domains
HIG1

Transcriptome

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

Promoters
RGD ID:13696392
Promoter ID:EPDNEW_R6917
Type:multiple initiation site
Name:Higd1a_1
Description:HIG1 hypoxia inducible domain family, member 1A
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_6.08130,491,885 - 130,491,945EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 129716548 129716549 C G snv SR/JrHsd (MCW)
8 129717173 129717174 T C snv Crl:SD (UDEL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620215 AgrOrtholog
Ensembl Genes ENSRNOG00000019428 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000061362 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000064114 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6890532 IMAGE-MGC_LOAD
InterPro Hypoxia_induced_domain UniProtKB/Swiss-Prot
KEGG Report rno:140937 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72714 IMAGE-MGC_LOAD
NCBI Gene 140937 ENTREZGENE
Pfam HIG_1_N UniProtKB/Swiss-Prot
PhenoGen Higd1a PhenoGen
PROSITE HIG1 UniProtKB/Swiss-Prot
UniProt HIG1A_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6PCV5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-05-18 Higd1a  HIG1 hypoxia inducible domain family, member 1A  Higd1a  HIG1 domain family, member 1A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-12-20 Higd1a  HIG1 domain family, member 1A  Hig1  hypoxia induced gene 1  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2002-08-07 Hig1  hypoxia induced gene 1      Symbol and Name status set to provisional 70820 PROVISIONAL