Human Gene HOXA7 (ENST00000242159.5_7) from GENCODE V47lift37
  Description: homeobox A7 (from RefSeq NM_006896.4)
Gencode Transcript: ENST00000242159.5_7
Gencode Gene: ENSG00000122592.8_13
Transcript (Including UTRs)
   Position: hg19 chr7:27,193,335-27,196,294 Size: 2,960 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr7:27,194,528-27,196,164 Size: 1,637 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:27,193,335-27,196,294)mRNA (may differ from genome)Protein (230 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HXA7_HUMAN
DESCRIPTION: RecName: Full=Homeobox protein Hox-A7; AltName: Full=Homeobox protein Hox 1.1; AltName: Full=Homeobox protein Hox-1A;
FUNCTION: Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the Antp homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.

-  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: HOXA7
Diseases sorted by gene-association score: oculoauricular syndrome (2), clivus chordoma (2), leukemia, acute myeloid (0)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 12.25 RPKM in Adrenal Gland
Total median expression: 133.96 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 -28.30130-0.218 Picture PostScript Text
3' UTR -349.801193-0.293 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
IPR017995 - Homeobox_antennapedia
IPR001827 - Homeobox_Antennapedia_CS
IPR017970 - Homeobox_CS
IPR020479 - Homeobox_metazoa
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeodomain

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on P31268
FrontTopSide
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0008134 transcription factor binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001525 angiogenesis
GO:0001953 negative regulation of cell-matrix adhesion
GO:0002686 negative regulation of leukocyte migration
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0009952 anterior/posterior pattern specification
GO:0045617 negative regulation of keratinocyte differentiation
GO:0045656 negative regulation of monocyte differentiation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048704 embryonic skeletal system morphogenesis
GO:0048863 stem cell differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0031965 nuclear membrane


-  Descriptions from all associated GenBank mRNAs
  LF207142 - JP 2014500723-A/14645: Polycomb-Associated Non-Coding RNAs.
LF362362 - JP 2014500723-A/169865: Polycomb-Associated Non-Coding RNAs.
JD331185 - Sequence 312209 from Patent EP1572962.
JD042263 - Sequence 23287 from Patent EP1572962.
JD240866 - Sequence 221890 from Patent EP1572962.
JD038300 - Sequence 19324 from Patent EP1572962.
JD036573 - Sequence 17597 from Patent EP1572962.
AF026397 - Homo sapiens homeobox transcription factor HOXA7 (HOXA7) mRNA, complete cds.
BC061916 - Homo sapiens cDNA clone IMAGE:4367439, containing frame-shift errors.
JD520687 - Sequence 501711 from Patent EP1572962.
JD314070 - Sequence 295094 from Patent EP1572962.
JD042643 - Sequence 23667 from Patent EP1572962.
BC140401 - Synthetic construct Homo sapiens clone IMAGE:100014451, MGC:173161 homeobox A7 (HOXA7) mRNA, encodes complete protein.
BC148692 - Synthetic construct Homo sapiens clone IMAGE:100015699, MGC:183154 homeobox A7 (HOXA7) mRNA, encodes complete protein.
AB463748 - Synthetic construct DNA, clone: pF1KB9691, Homo sapiens HOXA7 gene for homeobox A7, without stop codon, in Flexi system.
LF362363 - JP 2014500723-A/169866: Polycomb-Associated Non-Coding RNAs.
LF362364 - JP 2014500723-A/169867: Polycomb-Associated Non-Coding RNAs.
LF212031 - JP 2014500723-A/19534: Polycomb-Associated Non-Coding RNAs.
LF362365 - JP 2014500723-A/169868: Polycomb-Associated Non-Coding RNAs.
LF362366 - JP 2014500723-A/169869: Polycomb-Associated Non-Coding RNAs.
MA442719 - JP 2018138019-A/14645: Polycomb-Associated Non-Coding RNAs.
MA597939 - JP 2018138019-A/169865: Polycomb-Associated Non-Coding RNAs.
MA597940 - JP 2018138019-A/169866: Polycomb-Associated Non-Coding RNAs.
MA597941 - JP 2018138019-A/169867: Polycomb-Associated Non-Coding RNAs.
MA447608 - JP 2018138019-A/19534: Polycomb-Associated Non-Coding RNAs.
MA597942 - JP 2018138019-A/169868: Polycomb-Associated Non-Coding RNAs.
MA597943 - JP 2018138019-A/169869: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_keratinocytePathway - Keratinocyte Differentiation

-  Other Names for This Gene
  Alternate Gene Symbols: A4D191, ENST00000242159.1, ENST00000242159.2, ENST00000242159.3, ENST00000242159.4, HOX1A, HXA7_HUMAN, NM_006896, O43368, O43486, O95655, P31268, Q9NSC8, Q9UDM1, uc317ejq.1, uc317ejq.2
UCSC ID: ENST00000242159.5_7
RefSeq Accession: NM_006896.4
Protein: P31268 (aka HXA7_HUMAN)

-  Gene Model Information
  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.