Human Gene HOXA5 (ENST00000222726.4) from GENCODE V44
  Description: Homo sapiens homeobox A5 (HOXA5), mRNA. (from RefSeq NM_019102)
RefSeq Summary (NM_019102): In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. Methylation of this gene may result in the loss of its expression and, since the encoded protein upregulates the tumor suppressor p53, this protein may play an important role in tumorigenesis. [provided by RefSeq, Jul 2008]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Gencode Transcript: ENST00000222726.4
Gencode Gene: ENSG00000106004.5
Transcript (Including UTRs)
   Position: hg38 chr7:27,141,052-27,143,681 Size: 2,630 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg38 chr7:27,141,835-27,143,607 Size: 1,773 Coding Exon Count: 2 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr7:27,141,052-27,143,681)mRNA (may differ from genome)Protein (270 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Homeobox protein Hox-A5; AltName: Full=Homeobox protein Hox-1C;
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. Also binds to its own promoter. Binds specifically to the motif 5'-CYYNATTA[TG]Y-3'.
DEVELOPMENTAL STAGE: Expressed during embryogenesis and in adult kidney.
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: HOXA5
Diseases sorted by gene-association score: mediastinal malignant lymphoma (11), mediastinal gray zone lymphoma (8), embryonal carcinoma (5)

-  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: 41.14 RPKM in Fallopian Tube
Total median expression: 260.28 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 -9.0074-0.122 Picture PostScript Text
3' UTR -167.20783-0.214 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 - Homeobox domain

ModBase Predicted Comparative 3D Structure on P20719
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 BrowserNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI Ensembl   
Protein Sequence Protein Sequence   
Alignment Alignment   

-  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:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0001501 skeletal system development
GO:0002009 morphogenesis of an epithelium
GO:0003016 respiratory system process
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:0007389 pattern specification process
GO:0007585 respiratory gaseous exchange
GO:0009952 anterior/posterior pattern specification
GO:0010870 positive regulation of receptor biosynthetic process
GO:0016477 cell migration
GO:0016525 negative regulation of angiogenesis
GO:0030324 lung development
GO:0030878 thyroid gland development
GO:0033599 regulation of mammary gland epithelial cell proliferation
GO:0035264 multicellular organism growth
GO:0043065 positive regulation of apoptotic process
GO:0045639 positive regulation of myeloid cell differentiation
GO:0045647 negative regulation of erythrocyte differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048286 lung alveolus development
GO:0048704 embryonic skeletal system morphogenesis
GO:0048706 embryonic skeletal system development
GO:0060435 bronchiole development
GO:0060439 trachea morphogenesis
GO:0060441 epithelial tube branching involved in lung morphogenesis
GO:0060480 lung goblet cell differentiation
GO:0060481 lobar bronchus epithelium development
GO:0060484 lung-associated mesenchyme development
GO:0060535 trachea cartilage morphogenesis
GO:0060536 cartilage morphogenesis
GO:0060574 intestinal epithelial cell maturation
GO:0060638 mesenchymal-epithelial cell signaling
GO:0060644 mammary gland epithelial cell differentiation
GO:0060749 mammary gland alveolus development
GO:0060764 cell-cell signaling involved in mammary gland development

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  DQ893761 - Synthetic construct Homo sapiens clone IMAGE:100008221; FLH164294.01L; RZPDo839E10161D homeobox A5 (HOXA5) gene, encodes complete protein.
JD112823 - Sequence 93847 from Patent EP1572962.
JD292519 - Sequence 273543 from Patent EP1572962.
BC013682 - Homo sapiens homeobox A5, mRNA (cDNA clone MGC:9376 IMAGE:3863578), complete cds.
CR542256 - Homo sapiens full open reading frame cDNA clone RZPDo834D0726D for gene HOXA5, homeo box A5; complete cds, incl. stopcodon.
DQ890593 - Synthetic construct clone IMAGE:100003223; FLH164298.01X; RZPDo839E10162D homeobox A5 (HOXA5) gene, encodes complete protein.
KJ891377 - Synthetic construct Homo sapiens clone ccsbBroadEn_00771 HOXA5 gene, encodes complete protein.
BT009744 - Homo sapiens homeo box A5 mRNA, complete cds.
AB587591 - Synthetic construct DNA, clone: pF1KB8923, Homo sapiens HOXA5 gene for homeobox A5, without stop codon, in Flexi system.
CR542277 - Homo sapiens full open reading frame cDNA clone RZPDo834G0826D for gene HOXA5, homeo box A5; complete cds, without stopcodon.

-  Other Names for This Gene
  Alternate Gene Symbols: A4D179, ENST00000222726.1, ENST00000222726.2, ENST00000222726.3, HOX1C, HXA5_HUMAN, NM_019102, O43367, P20719, Q96CY6, uc003syn.1, uc003syn.2, uc003syn.3
UCSC ID: ENST00000222726.4
RefSeq Accession: NM_019102
Protein: P20719 (aka HXA5_HUMAN)
CCDS: CCDS5406.1

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