Free for academic non-profit institutions. Other users need a Commercial license

Aliases for HOXA11 Gene

Aliases for HOXA11 Gene

  • Homeobox A11 2 3 5
  • Homeobox Protein Hox-1I 3 4
  • HOX1I 3 4
  • Homeobox Protein Hox-A11 3
  • Homeobox Protein HOXA11 3
  • Homeo Box A11 2
  • Homeo Box 1I 3
  • RUSAT1 3
  • HOX1 3

External Ids for HOXA11 Gene

Previous HGNC Symbols for HOXA11 Gene

  • HOX1I
  • HOX1

Previous GeneCards Identifiers for HOXA11 Gene

  • GC07M026864
  • GC07M026929
  • GC07M026963
  • GC07M026994
  • GC07M027187
  • GC07M027220
  • GC07M027182
  • GC07M027183
  • GC07M027190

Summaries for HOXA11 Gene

Entrez Gene Summary for HOXA11 Gene

  • 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 involved in the regulation of uterine development and is required for female fertility. Mutations in this gene can cause radio-ulnar synostosis with amegakaryocytic thrombocytopenia. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXA11 Gene

HOXA11 (Homeobox A11) is a Protein Coding gene. Diseases associated with HOXA11 include Radioulnar Synostosis With Amegakaryocytic Thrombocytopenia 1 and Radio-Ulnar Synostosis-Amegakaryocytic Thrombocytopenia Syndrome. Among its related pathways are Transcriptional misregulation in cancer. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HOXD11.

UniProtKB/Swiss-Prot for HOXA11 Gene

  • Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Gene Wiki entry for HOXA11 Gene

Additional gene information for HOXA11 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXA11 Gene

Genomics for HOXA11 Gene

GeneHancer (GH) Regulatory Elements for HOXA11 Gene

Promoters and enhancers for HOXA11 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07J027181 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.9 904 5.1 HDGF PKNOX1 FEZF1 ZNF2 YY1 GLIS2 ELK1 KLF7 REST SMARCB1 HOXA11-AS ENSG00000273961 ENSG00000276496 ENSG00000278334 GC07P027266 GC07P027267 HOXA11 HOXA10-AS HOTAIRM1 HOXA10
GH07J027095 Promoter/Enhancer 3.4 VISTA UCNEbase EPDnew FANTOM5 Ensembl ENCODE dbSUPER 14.3 +47.0 47028 86.3 MLX FEZF1 DMAP1 YY1 ZNF213 ZNF143 SP3 NFYC SSRP1 ZNF610 HOXA2 HOXA9 HOXA10 HOXA1 HOXA3 HOXA6 HOXA4 HOXA5 HOXA7 HNRNPA2B1
GH07J027920 Enhancer 1 Ensembl ENCODE 10.7 -736.1 -736092 0.6 MZF1 SIN3A BMI1 FEZF1 ZNF2 RAD21 RFX5 ZNF335 ZNF213 ZSCAN5C ENSG00000253508 HOTTIP HOXA13 HOXA11 HOXA11-AS HOXA10 HOXA9 ENSG00000253308 EVX1 EVX1-AS
GH07J028082 Enhancer 1.1 FANTOM5 Ensembl ENCODE 9.7 -898.5 -898460 2.6 FOXA2 RXRA CEBPB REST EP300 RFX5 YY1 SP1 JUND ATF3 JAZF1 JAZF1-AS1 HOXA11 HOXA11-AS HOXA10 HOXA9 HOXA13 ENSG00000253508 HOTTIP EVX1-AS
GH07J028018 Enhancer 1 Ensembl ENCODE 10.3 -834.5 -834530 2.2 RB1 SIN3A ZNF2 RAD21 RFX5 ZNF143 RCOR1 RUNX3 CREM DEK ENSG00000253508 HOXA13 HOTTIP HOXA10 HOXA11-AS HOXA11 HOXA9 PIR54187 PIR39851 JAZF1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOXA11 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXA11 gene promoter:
  • c-Jun
  • ATF-2
  • p53
  • MyoD
  • C/EBPalpha
  • YY1

Genomic Locations for HOXA11 Gene

Genomic Locations for HOXA11 Gene
4,067 bases
Minus strand
4,067 bases
Minus strand

Genomic View for HOXA11 Gene

Genes around HOXA11 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXA11 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXA11 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXA11 Gene

Proteins for HOXA11 Gene

  • Protein details for HOXA11 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Hox-A11
    Protein Accession:
    Secondary Accessions:
    • A4D190

    Protein attributes for HOXA11 Gene

    313 amino acids
    Molecular mass:
    34486 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HOXA11 Gene

Post-translational modifications for HOXA11 Gene

  • Ubiquitination at isoforms=72
  • Modification sites at PhosphoSitePlus

Other Protein References for HOXA11 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXA11 Gene

Domains & Families for HOXA11 Gene

Gene Families for HOXA11 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for HOXA11 Gene

Suggested Antigen Peptide Sequences for HOXA11 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Abd-B homeobox family.
  • Belongs to the Abd-B homeobox family.
genes like me logo Genes that share domains with HOXA11: view

Function for HOXA11 Gene

Molecular function for HOXA11 Gene

UniProtKB/Swiss-Prot 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.
GENATLAS Biochemistry:
homeo box A11(1I),homologous to mouse Hox-1.9

Phenotypes From GWAS Catalog for HOXA11 Gene

Gene Ontology (GO) - Molecular Function for HOXA11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0003677 DNA binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXA11: view
genes like me logo Genes that share phenotypes with HOXA11: view

Human Phenotype Ontology for HOXA11 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HOXA11 Gene

MGI Knock Outs for HOXA11:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOXA11

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for HOXA11 Gene

Localization for HOXA11 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXA11 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HOXA11 gene
Compartment Confidence
nucleus 5
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HOXA11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0005667 transcription factor complex ISS,IEA --
GO:0032991 protein-containing complex ISS,IEA --
GO:0032993 protein-DNA complex IEA,ISS --
genes like me logo Genes that share ontologies with HOXA11: view

Pathways & Interactions for HOXA11 Gene

genes like me logo Genes that share pathways with HOXA11: view

Pathways by source for HOXA11 Gene

1 KEGG pathway for HOXA11 Gene

Gene Ontology (GO) - Biological Process for HOXA11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IEA,ISS --
GO:0001656 metanephros development IEA --
GO:0001658 branching involved in ureteric bud morphogenesis IEA,ISS --
GO:0001759 organ induction IEA --
GO:0006351 transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with HOXA11: view

No data available for SIGNOR curated interactions for HOXA11 Gene

Drugs & Compounds for HOXA11 Gene

(2) Drugs for HOXA11 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with HOXA11: view

Transcripts for HOXA11 Gene

mRNA/cDNA for HOXA11 Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(69) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HOXA11 Gene

Homeobox A11:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOXA11

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXA11 Gene

No ASD Table

Relevant External Links for HOXA11 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOXA11 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXA11 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXA11 Gene

This gene is overexpressed in Uterus (x14.2), Cervix - Endocervix (x6.9), Cervix - Ectocervix (x5.3), and Colon - Sigmoid (x4.7).

NURSA nuclear receptor signaling pathways regulating expression of HOXA11 Gene:


SOURCE GeneReport for Unigene cluster for HOXA11 Gene:


Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXA11 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • cardiovascular
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
  • pelvis
  • arm
  • digit
  • femur
  • finger
  • foot
  • forearm
  • hand
  • hip
  • lower limb
  • radius
  • thigh
  • toe
  • ulna
  • upper limb
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with HOXA11: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES for HOXA11 Gene

Orthologs for HOXA11 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HOXA11 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HOXA11 34 33
  • 95.74 (n)
(Bos Taurus)
Mammalia HOXA11 34 33
  • 94.87 (n)
(Mus musculus)
Mammalia Hoxa11 16 34 33
  • 94.64 (n)
(Rattus norvegicus)
Mammalia Hoxa11 33
  • 94.32 (n)
(Canis familiaris)
Mammalia HOXA11 34 33
  • 91.37 (n)
(Monodelphis domestica)
Mammalia HOXA11 34
  • 82 (a)
(Ornithorhynchus anatinus)
Mammalia HOXA11 34
  • 80 (a)
(Gallus gallus)
Aves HOXA11 34
  • 84 (a)
LOC100858967 33
  • 81.42 (n)
(Anolis carolinensis)
Reptilia HOXA11 34
  • 69 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxa11 33
  • 76.78 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.16037 33
(Danio rerio)
Actinopterygii hoxa11b 34 33 33
  • 73.95 (n)
hoxa11a 34
  • 67 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7890 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 12 (a)
Species where no ortholog for HOXA11 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HOXA11 Gene

Gene Tree for HOXA11 (if available)
Gene Tree for HOXA11 (if available)
Evolutionary constrained regions (ECRs) for HOXA11: view image

Paralogs for HOXA11 Gene

(9) SIMAP similar genes for HOXA11 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with HOXA11: view

Variants for HOXA11 Gene

Sequence variations from dbSNP and Humsavar for HOXA11 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs864321666 pathogenic, Radioulnar synostosis with amegakaryocytic thrombocytopenia 27,182,866(-) TT/T coding_sequence_variant, frameshift
rs115808703 likely-benign, not specified 27,182,898(-) G/A coding_sequence_variant, synonymous_variant
rs1085307723 uncertain-significance, not specified 27,184,520(-) C/T coding_sequence_variant, missense_variant
rs1001749900 -- 27,183,536(-) A/C intron_variant
rs1001802119 -- 27,183,165(-) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HOXA11 Gene

Variant ID Type Subtype PubMed ID
dgv1094n67 CNV gain 20364138
nsv5675 CNV insertion 18451855
nsv606465 CNV loss 21841781
nsv606468 CNV loss 21841781
nsv606469 CNV loss 21841781
nsv7393 OTHER inversion 18451855
nsv824042 CNV gain 20364138

Variation tolerance for HOXA11 Gene

Residual Variation Intolerance Score: 63.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.12; 22.81% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXA11 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXA11 Gene

Disorders for HOXA11 Gene

MalaCards: The human disease database

(10) MalaCards diseases for HOXA11 Gene - From: LncRNADisease, HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards


  • Radioulnar synostosis with amegakaryocytic thrombocytopenia 1 (RUSAT1) [MIM:605432]: The syndrome consists of an unusual association of bone marrow failure and skeletal defects. Patients have the same skeletal defects, the proximal fusion of the radius and ulna, resulting in extremely limited pronation and supination of the forearm. Some patients have also symptomatic thrombocytopenia, with bruising and bleeding problems since birth, necessitating correction by bone marrow or umbilical-cord stem-cell transplantation. {ECO:0000269 PubMed:11101832}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for HOXA11

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HOXA11: view

No data available for Genatlas for HOXA11 Gene

Publications for HOXA11 Gene

  1. Absence of mutations in the HOXA11 and HOXD11 genes in children with congenital renal malformations. (PMID: 19255789) Bouba I … Georgiou I (Pediatric nephrology (Berlin, Germany) 2009) 3 22 44 58
  2. Amegakaryocytic thrombocytopenia and radio-ulnar synostosis are associated with HOXA11 mutation. (PMID: 11101832) Thompson AA … Nguyen LT (Nature genetics 2000) 3 4 22 58
  3. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PMID: 19453261) Yerges LM … MrOS Research Group (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2009) 3 44 58
  4. Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot. (PMID: 19938081) Ester AR … Hecht JT (American journal of medical genetics. Part A 2009) 3 44 58
  5. HOXA11 promotes fibroblast proliferation and regulates p53 in uterosacral ligaments. (PMID: 19372592) Connell KA … Taylor HS (Reproductive sciences (Thousand Oaks, Calif.) 2009) 3 22 58

Products for HOXA11 Gene

Sources for HOXA11 Gene

Loading form....