Human Gene HIF1A (uc021rua.1)
  Description: Homo sapiens hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) (HIF1A), transcript variant 3, mRNA.
RefSeq Summary (NM_001243084): This gene encodes the alpha subunit of transcription factor hypoxia-inducible factor-1 (HIF-1), which is a heterodimer composed of an alpha and a beta subunit. HIF-1 functions as a master regulator of cellular and systemic homeostatic response to hypoxia by activating transcription of many genes, including those involved in energy metabolism, angiogenesis, apoptosis, and other genes whose protein products increase oxygen delivery or facilitate metabolic adaptation to hypoxia. HIF-1 thus plays an essential role in embryonic vascularization, tumor angiogenesis and pathophysiology of ischemic disease. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2011].
Transcript (Including UTRs)
   Position: hg19 chr14:62,164,340-62,214,977 Size: 50,638 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr14:62,164,569-62,213,803 Size: 49,235 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:62,164,340-62,214,977)mRNA (may differ from genome)Protein (850 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: C0LZJ3_HUMAN
DESCRIPTION: SubName: Full=Hypoxia-inducible factor 1 alpha isoform I.3; SubName: Full=Hypoxia-inducible factor 1-alpha;
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
SIMILARITY: Contains 1 basic helix-loop-helix (bHLH) domain.
SIMILARITY: Contains 2 PAS (PER-ARNT-SIM) domains.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HIF1A
CDC HuGE Published Literature: HIF1A
Positive Disease Associations: Blood Pressure , CD40 Ligand , cervical cancer endometrial cancer ovarian cancer , colorectal cancer , diabetes, type 2; retinopathy, diabetic , esophageal cancer , HIF-1alpha protein expression , hypoxia , kidney cancer , osteonecrosis , oxygen consumption , stroke, ischemic , Uric Acid
Related Studies:
  1. Blood Pressure
    , , . [PubMed 0]
  2. CD40 Ligand
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
  3. cervical cancer endometrial cancer ovarian cancer
    Konac, E. et al. 2007, An investigation of relationships between hypoxia-inducible factor-1alpha gene polymorphisms and ovarian, cervical and endometrial cancers, Cancer Detect Prev 2007. [PubMed 17418979]
    Our results suggest that the C1772T polymorphism of the HIF-1 alpha may be associated with cervical and endometrial cancers.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: HIF1A
Diseases sorted by gene-association score: hypoxia (133), retinal ischemia (27), renal clear cell carcinoma (14), fumarate hydratase deficiency (13), transitional meningioma (12), kidney cancer (11), intravascular papillary endothelial hyperplasia (10), renal cell carcinoma (9), varicocele (9), polycythemia (9), limb ischemia (9), erythrocytosis, familial, 2 (8), leiomyomatosis and renal cell cancer (7), degenerative disc disease (7), nodular prostate (7), clear cell renal cell carcinoma (7), ameloblastic carcinoma (7), cholesteatoma of middle ear (6), colon adenoma (6), von hippel-lindau syndrome (6), hepatocellular carcinoma (6), acute mountain sickness (6), familial renal papillary carcinoma (5), balo concentric sclerosis (5), pericardial effusion (5), ischemia (5), lung cancer (5), colorectal cancer (4), hydronephrosis (4), congenital muscular dystrophy due to lmna mutation (4), malignant dermis tumor (4), retinal hemangioblastoma (4), appendix adenocarcinoma (4), endometrial cancer (3), pulmonary hypertension (3), deficiency anemia (3), prostate cancer (3), cervical cancer, somatic (3), ovarian cancer, somatic (3), oral squamous cell carcinoma (3), nasopharyngeal carcinoma (2), pancreatic cancer (2), squamous cell carcinoma, head and neck (2), breast cancer (2), esophageal cancer (2), lung cancer susceptibility 3 (2), myocardial infarction (1), exudative vitreoretinopathy 1 (1)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 157.93 RPKM in Cells - Cultured fibroblasts
Total median expression: 1446.00 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 -44.20229-0.193 Picture PostScript Text
3' UTR -239.441174-0.204 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
IPR001321 - HIF-1_alpha
IPR014887 - HIF-1_TAD_C
IPR021537 - HIF_alpha_subunit
IPR011598 - HLH_dom
IPR001610 - PAC
IPR000014 - PAS
IPR013767 - PAS_fold
IPR013655 - PAS_fold_3

Pfam Domains:
PF00989 - PAS fold
PF08447 - PAS fold
PF08778 - HIF-1 alpha C terminal transactivation domain
PF11413 - Hypoxia-inducible factor-1
PF13426 - PAS domain
PF14598 - PAS domain

SCOP Domains:
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain)

ModBase Predicted Comparative 3D Structure on C0LZJ3
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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
No orthologGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Descriptions from all associated GenBank mRNAs
  AK296876 - Homo sapiens cDNA FLJ54364 complete cds, highly similar to Hypoxia-inducible factor 1 alpha.
AK304436 - Homo sapiens cDNA FLJ57096 complete cds, highly similar to Hypoxia-inducible factor 1 alpha.
AK299551 - Homo sapiens cDNA FLJ59406 complete cds, highly similar to Hypoxia-inducible factor 1 alpha.
AK304315 - Homo sapiens cDNA FLJ55752 complete cds, highly similar to Hypoxia-inducible factor 1 alpha.
FW408286 - NUCLEIC ACID COMPOUNDS FOR INHIBITING HIF1A GENE EXPRESSION AND USES THEREOF.
FW408287 - NUCLEIC ACID COMPOUNDS FOR INHIBITING HIF1A GENE EXPRESSION AND USES THEREOF.
BX648795 - Homo sapiens mRNA; cDNA DKFZp686O09143 (from clone DKFZp686O09143).
U29165 - Human MOP1 mRNA, complete cds.
BC012527 - Homo sapiens hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor), mRNA (cDNA clone MGC:10483 IMAGE:3842146), complete cds.
AK312397 - Homo sapiens cDNA, FLJ92729, highly similar to Homo sapiens hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) (HIF1A), mRNA.
AB733094 - Homo sapiens HIF-1A mRNA for hypoxia-inducible factor1alpha, complete cds.
AB073325 - Homo sapiens HIF1A mRNA for hypoxia-inducible factor 1 alpha variant, complete cds.
U22431 - Human hypoxia-inducible factor 1 alpha (HIF-1 alpha) mRNA, complete cds.
AB500182 - Homo sapiens HIF1A mRNA for hypoxia-inducible factor 1, alpha subunit, variant K12NR, complete cds.
AF207601 - Homo sapiens cell-line GM11201 hypoxia-inducible factor 1 alpha (HIF1A) mRNA, complete cds.
AF207602 - Homo sapiens cell-line GM11197 hypoxia-inducible factor 1 alpha (HIF1A) mRNA, complete cds.
AB385144 - Synthetic construct DNA, clone: pF1KB5648, Homo sapiens HIF1A gene for hypoxia-inducible factor 1 alpha, complete cds, without stop codon, in Flexi system.
KJ896971 - Synthetic construct Homo sapiens clone ccsbBroadEn_06365 HIF1A gene, encodes complete protein.
KR710293 - Synthetic construct Homo sapiens clone CCSBHm_00011107 HIF1A (HIF1A) mRNA, encodes complete protein.
KR710294 - Synthetic construct Homo sapiens clone CCSBHm_00011108 HIF1A (HIF1A) mRNA, encodes complete protein.
BT009776 - Homo sapiens hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) mRNA, complete cds.
AF304431 - Homo sapiens hypoxia-inducible factor 1 alpha subunit (HIF1A) mRNA, complete cds.
FJ790247 - Homo sapiens hypoxia-inducible factor 1 alpha isoform I.3 (HIF1A) mRNA, complete cds.
LZ221033 - WO 2017163391-A/9: Method of evaluating or selecting androgen receptor regulator specific to sebaceous gland in skin or hair follicle.
LZ221031 - WO 2017163391-A/7: Method of evaluating or selecting androgen receptor regulator specific to sebaceous gland in skin or hair follicle.
DQ975378 - Homo sapiens hypoxia-inducible factor 1 alpha subunit transcript variant 3-like (HIF1A) mRNA, partial sequence, alternatively spliced.
X72726 - H.sapiens tunp mRNA for transformation upregulated nuclear protein, exon D.
JD490881 - Sequence 471905 from Patent EP1572962.
JD400349 - Sequence 381373 from Patent EP1572962.
JD062765 - Sequence 43789 from Patent EP1572962.
AJ227916 - Homo sapiens partial mRNA; ID LG141-7A.
JD349463 - Sequence 330487 from Patent EP1572962.
JD549407 - Sequence 530431 from Patent EP1572962.
JD083405 - Sequence 64429 from Patent EP1572962.
MP119867 - Sequence 10 from Patent EP3444356.
MP119865 - Sequence 8 from Patent EP3444356.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04150 - mTOR signaling pathway
hsa05200 - Pathways in cancer
hsa05211 - Renal cell carcinoma

BioCarta from NCI Cancer Genome Anatomy Project
h_p53hypoxiaPathway - Hypoxia and p53 in the Cardiovascular system
h_eponfkbPathway - Erythropoietin mediated neuroprotection through NF-kB
h_vegfPathway - VEGF, Hypoxia, and Angiogenesis
h_hifPathway - Hypoxia-Inducible Factor in the Cardiovascular System

-  Other Names for This Gene
  Alternate Gene Symbols: C0LZJ3, C0LZJ3_HUMAN, NM_001243084, NP_001230013
UCSC ID: uc021rua.1
RefSeq Accession: NM_001243084
Protein: C0LZJ3 CCDS: CCDS58324.1, CCDS9753.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001243084.1
exon count: 15CDS single in 3' UTR: no RNA size: 3979
ORF size: 2553CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4916.00frame shift in genome: no % Coverage: 99.42
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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