Human Gene HIGD1A (ENST00000418900.6) from GENCODE V44
  Description: P49662:CASP4; NbExp=1; IntAct=EBI-1051940, EBI-1057327; Q9P286:PAK7; NbExp=1; IntAct=EBI-1051940, EBI-1051061; P14678:SNRPB; NbExp=1; IntAct=EBI-1051940, EBI-372458; (from UniProt Q9Y241)
Gencode Transcript: ENST00000418900.6
Gencode Gene: ENSG00000181061.14
Transcript (Including UTRs)
   Position: hg38 chr3:42,784,330-42,804,488 Size: 20,159 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg38 chr3:42,785,271-42,794,253 Size: 8,983 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:42,784,330-42,804,488)mRNA (may differ from genome)Protein (93 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
HPRDLynxMalacardsMGIneXtProtPubMed
ReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: HIG1A_HUMAN
DESCRIPTION: RecName: Full=HIG1 domain family member 1A; AltName: Full=Hypoxia-inducible gene 1 protein;
INTERACTION: P49662:CASP4; NbExp=1; IntAct=EBI-1051940, EBI-1057327; Q9P286:PAK7; NbExp=1; IntAct=EBI-1051940, EBI-1051061; P14678:SNRPB; NbExp=1; IntAct=EBI-1051940, EBI-372458;
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
INDUCTION: By hypoxia.
SIMILARITY: Contains 1 HIG1 domain.
SEQUENCE CAUTION: Sequence=BG400624; Type=Frameshift; Positions=32;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: HIGD1A
Diseases sorted by gene-association score: hypoxia (9)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 123.22 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 3479.61 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -23.6099-0.238 Picture PostScript Text
3' UTR -215.80941-0.229 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007667 - Hypoxia_induced_domain

Pfam Domains:
PF04588 - Hypoxia induced protein conserved region

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2LOM - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9Y241
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0043066 negative regulation of apoptotic process
GO:0055114 oxidation-reduction process
GO:0061418 regulation of transcription from RNA polymerase II promoter in response to hypoxia

Cellular Component:
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031966 mitochondrial membrane
GO:0032991 macromolecular complex
GO:0070469 respiratory chain


-  Descriptions from all associated GenBank mRNAs
  BC009594 - Homo sapiens HIG1 domain family, member 1A, mRNA (cDNA clone MGC:14680 IMAGE:4109190), complete cds.
BC000601 - Homo sapiens HIG1 domain family, member 1A, mRNA (cDNA clone MGC:1248 IMAGE:3346355), complete cds.
BC070277 - Homo sapiens HIG1 domain family, member 1A, mRNA (cDNA clone MGC:88270 IMAGE:4686431), complete cds.
AK225571 - Homo sapiens mRNA for HIG1 domain family, member 1A variant, clone: LNF00461.
LP895462 - Sequence 326 from Patent EP3253886.
LF208676 - JP 2014500723-A/16179: Polycomb-Associated Non-Coding RNAs.
MA444253 - JP 2018138019-A/16179: Polycomb-Associated Non-Coding RNAs.
AF145385 - Homo sapiens hypoxia-inducbile gene 1 (HIG1) mRNA, complete cds.
AF077034 - Homo sapiens HSPC010 mRNA, complete cds.
AL110233 - Homo sapiens mRNA; cDNA DKFZp564K247 (from clone DKFZp564K247).
BC009583 - Homo sapiens HIG1 domain family, member 1A, mRNA (cDNA clone MGC:14641 IMAGE:4093421), complete cds.
LF378919 - JP 2014500723-A/186422: Polycomb-Associated Non-Coding RNAs.
MA614496 - JP 2018138019-A/186422: Polycomb-Associated Non-Coding RNAs.
JD359066 - Sequence 340090 from Patent EP1572962.
JD299954 - Sequence 280978 from Patent EP1572962.
JD313596 - Sequence 294620 from Patent EP1572962.
LF378920 - JP 2014500723-A/186423: Polycomb-Associated Non-Coding RNAs.
MA614497 - JP 2018138019-A/186423: Polycomb-Associated Non-Coding RNAs.
JD027084 - Sequence 8108 from Patent EP1572962.
JD030190 - Sequence 11214 from Patent EP1572962.
LF378921 - JP 2014500723-A/186424: Polycomb-Associated Non-Coding RNAs.
MA614498 - JP 2018138019-A/186424: Polycomb-Associated Non-Coding RNAs.
JD479296 - Sequence 460320 from Patent EP1572962.
JD042191 - Sequence 23215 from Patent EP1572962.
LF378922 - JP 2014500723-A/186425: Polycomb-Associated Non-Coding RNAs.
MA614499 - JP 2018138019-A/186425: Polycomb-Associated Non-Coding RNAs.
JD431371 - Sequence 412395 from Patent EP1572962.
JD022142 - Sequence 3166 from Patent EP1572962.
JD022143 - Sequence 3167 from Patent EP1572962.
JD022144 - Sequence 3168 from Patent EP1572962.
JD021744 - Sequence 2768 from Patent EP1572962.
JD034774 - Sequence 15798 from Patent EP1572962.
JD030314 - Sequence 11338 from Patent EP1572962.
JD031602 - Sequence 12626 from Patent EP1572962.
AK225461 - Homo sapiens mRNA for HIG1 domain family, member 1A variant, clone: HSI05820.
JD436297 - Sequence 417321 from Patent EP1572962.
AK311815 - Homo sapiens cDNA, FLJ92076, Homo sapiens likely ortholog of mouse hypoxia induced gene 1(HIG1), mRNA.
CR457385 - Homo sapiens full open reading frame cDNA clone RZPDo834E0510D for gene HIG1, likely ortholog of mouse hypoxia induced gene 1; complete cds, incl. stopcodon.
KJ893504 - Synthetic construct Homo sapiens clone ccsbBroadEn_02898 HIGD1A gene, encodes complete protein.
AM393830 - Synthetic construct Homo sapiens clone IMAGE:100001998 for hypothetical protein (HIGD1A gene).
AB528289 - Synthetic construct DNA, clone: pF1KE0160, Homo sapiens HIGD1A gene for HIG1 hypoxia inducible domain family, member 1A, without stop codon, in Flexi system.
LF378923 - JP 2014500723-A/186426: Polycomb-Associated Non-Coding RNAs.
MA614500 - JP 2018138019-A/186426: Polycomb-Associated Non-Coding RNAs.
LF378924 - JP 2014500723-A/186427: Polycomb-Associated Non-Coding RNAs.
MA614501 - JP 2018138019-A/186427: Polycomb-Associated Non-Coding RNAs.
JD084260 - Sequence 65284 from Patent EP1572962.
JD358619 - Sequence 339643 from Patent EP1572962.
JD183724 - Sequence 164748 from Patent EP1572962.
LF208678 - JP 2014500723-A/16181: Polycomb-Associated Non-Coding RNAs.
MA444255 - JP 2018138019-A/16181: Polycomb-Associated Non-Coding RNAs.
JD294689 - Sequence 275713 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y241 (Reactome details) participates in the following event(s):

R-HSA-1234158 Regulation of gene expression by Hypoxia-inducible Factor
R-HSA-1234174 Regulation of Hypoxia-inducible Factor (HIF) by oxygen
R-HSA-2262749 Cellular response to hypoxia
R-HSA-2262752 Cellular responses to stress
R-HSA-8953897 Cellular responses to external stimuli

-  Other Names for This Gene
  Alternate Gene Symbols: BC070277, ENST00000418900.1, ENST00000418900.2, ENST00000418900.3, ENST00000418900.4, ENST00000418900.5, HIG1, HIG1A_HUMAN, HSPC010, Q9UFZ2, Q9Y241, uc003cma.1, uc003cma.2, uc003cma.3, uc003cma.4, uc003cma.5
UCSC ID: ENST00000418900.6
RefSeq Accession: NM_001099669
Protein: Q9Y241 (aka HIG1A_HUMAN)
CCDS: CCDS43073.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.