HOXA9 homeobox A9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HOXA9provided by HGNC
Official Full Name: homeobox A9provided by HGNC
Primary source: HGNC:HGNC:5109
See related: Ensembl:ENSG00000078399 MIM:142956; AllianceGenome:HGNC:5109
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HOX1; ABD-B; HOX1G; HOX1.7
Summary: 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. This gene is highly similar to the abdominal-B (Abd-B) gene of Drosophila. A specific translocation event which causes a fusion between this gene and the NUP98 gene has been associated with myeloid leukemogenesis. Read-through transcription exists between this gene and the upstream homeobox A10 (HOXA10) gene.[provided by RefSeq, Mar 2011]
Expression: Biased expression in kidney (RPKM 13.0), endometrium (RPKM 8.0) and 11 other tissues See more
Orthologs: all
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Genomic context

Location:: 7p15.2

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (27162438..27165537, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (27298433..27301532, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (27202057..27205156, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9.
Title: RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9.
HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia.
Title: HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia.
Molecular regulators of HOXA9 in acute myeloid leukemia.
Title: Molecular regulators of HOXA9 in acute myeloid leukemia.
HOXA9 has the hallmarks of a biological switch with implications in blood cancers.
Title: HOXA9 has the hallmarks of a biological switch with implications in blood cancers.
Downregulation of hsa-miR-548d-3p and overexpression of HOXA9 in diffuse large B-cell lymphoma patients and the risk of R-CHOP chemotherapy resistance and disease progression.
Title: Downregulation of hsa-miR-548d-3p and overexpression of HOXA9 in diffuse large B-cell lymphoma patients and the risk of R-CHOP chemotherapy resistance and disease progression.
circ_0052184 Promotes Colorectal Cancer Progression via Targeting miR-604/HOXA9 Axis.
Title: circ_0052184 Promotes Colorectal Cancer Progression via Targeting miR-604/HOXA9 Axis.
HOXA9 Overexpression Contributes to Stem Cell Overpopulation That Drives Development and Growth of Colorectal Cancer.
Title: HOXA9 Overexpression Contributes to Stem Cell Overpopulation That Drives Development and Growth of Colorectal Cancer.
Circular RNA circFADS2 inhibits the progression of cutaneous squamous cell carcinoma by regulating miR-766-3p/HOXA9 axis.
Title: Circular RNA circFADS2 inhibits the progression of cutaneous squamous cell carcinoma by regulating miR-766-3p/HOXA9 axis.
Comprehensive Landscape of HOXA2, HOXA9, and HOXA10 as Potential Biomarkers for Predicting Progression and Prognosis in Prostate Cancer.
Title: Comprehensive Landscape of HOXA2, HOXA9, and HOXA10 as Potential Biomarkers for Predicting Progression and Prognosis in Prostate Cancer.
ALKBH5-mediated m6A modification of lncRNA KCNQ1OT1 triggers the development of LSCC via upregulation of HOXA9.
Title: ALKBH5-mediated m6A modification of lncRNA KCNQ1OT1 triggers the development of LSCC via upregulation of HOXA9.

Submit: New GeneRIF Correction See all GeneRIFs (175)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

ECD00507 (e-PCR)
- UniSTS:281618

RH80175 (e-PCR)
- UniSTS:84531

ECD00028 (e-PCR)
- UniSTS:281142

PMC15172P1 (e-PCR)
- UniSTS:271171

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:536646

HOXA9_991 (e-PCR)
- UniSTS:277318

HOXA9_V256 (e-PCR)
- UniSTS:277318

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:468837

ECD00619 (e-PCR)
- UniSTS:281728

RH18061 (e-PCR)
- UniSTS:50049

ECD00415 (e-PCR)
- UniSTS:281526

REN100605 (e-PCR)
- UniSTS:425402

REN100606 (e-PCR)
- UniSTS:425403

REN100607 (e-PCR)
- UniSTS:425404

REN100608 (e-PCR)
- UniSTS:425405

REN100609 (e-PCR)
- UniSTS:425406

REN100610 (e-PCR)
- UniSTS:425407

REN100611 (e-PCR)
- UniSTS:425408

REN100612 (e-PCR)
- UniSTS:425409

REN100613 (e-PCR)
- UniSTS:425410

REN100614 (e-PCR)
- UniSTS:425411

REN100619 (e-PCR)
- UniSTS:425416

REN100620 (e-PCR)
- UniSTS:425417

REN100621 (e-PCR)
- UniSTS:425418

REN100622 (e-PCR)
- UniSTS:425419

REN100623 (e-PCR)
- UniSTS:425420

REN100624 (e-PCR)
- UniSTS:425421

REN100625 (e-PCR)
- UniSTS:425422

REN100626 (e-PCR)
- UniSTS:425423

REN100627 (e-PCR)
- UniSTS:425424

REN100628 (e-PCR)
- UniSTS:425425

ECD00475 (e-PCR)
- UniSTS:281586

HOX1 (e-PCR)
- UniSTS:71932

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:516607

Readthrough HOXA10-HOXA9

Readthrough gene: HOXA10-HOXA9, Included gene: HOXA10

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
involved_in definitive hemopoiesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic forelimb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic skeletal system morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in endothelial cell activation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in male gonad development	IEA Inferred from Electronic Annotation more info
involved_in mammary gland development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of myeloid cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in prostate gland development	IEA Inferred from Electronic Annotation more info
involved_in proximal/distal pattern formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to testosterone	IEA Inferred from Electronic Annotation more info
involved_in single fertilization	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
involved_in uterus development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info
part_of transcription regulator complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: homeobox protein Hox-A9

Names: homeobox protein Hox-1G; homeodomain protein HOXA9

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029923.1 RefSeqGene

Range

4994..8093

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_152739.4 → NP_689952.1 homeobox protein Hox-A9

See identical proteins and their annotated locations for NP_689952.1

Status: REVIEWED

Source sequence(s)

AC004080, AW612618, BC006537, BG258601, CA442923

Consensus CDS

CCDS5409.1

UniProtKB/Swiss-Prot

O43369, O43429, P31269, Q99820

UniProtKB/TrEMBL

O75806

Related

ENSP00000343619.6, ENST00000343483.7

Conserved Domains (2) summary

pfam00046
Location:209 → 262

Homeobox; Homeobox domain

pfam04617
Location:1 → 193

Hox9_act; Hox9 activation region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

27162438..27165537 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

27298433..27301532 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_002142.3: Suppressed sequence

Description

NM_002142.3: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.