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Aliases for HOXD9 Gene

Aliases for HOXD9 Gene

  • Homeobox D9 2 3
  • HOX4C 3 4 6
  • Homeobox Protein Hox-5.2 3 4
  • Homeobox Protein Hox-4C 3 4
  • Homeo Box D9 2 3
  • Hox-4.3, Mouse, Homolog Of 3
  • Homeobox Protein Hox-D9 3
  • Hox-4.3 3
  • Hox-5.2 3
  • HOX4 3

External Ids for HOXD9 Gene

Previous Symbols for HOXD9 Gene

  • HOX4C
  • HOX4

Summaries for HOXD9 Gene

Entrez Gene Summary for HOXD9 Gene

  • This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located at 2q31-2q37 chromosome regions. Deletions that removed the entire HOXD gene cluster or 5' end of this cluster have been associated with severe limb and genital abnormalities. The exact role of this gene has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXD9 Gene

HOXD9 (Homeobox D9) is a Protein Coding gene. Diseases associated with HOXD9 include brachydactyly-syndactyly syndrome and syndactyly, type v. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is HOXD10.

UniProtKB/Swiss-Prot for HOXD9 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 HOXD9 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXD9 Gene

Genomics for HOXD9 Gene

Genomic Location for HOXD9 Gene

Start:
176,122,685 bp from pter
End:
176,124,937 bp from pter
Size:
2,253 bases
Orientation:
Plus strand

Genomic View for HOXD9 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HOXD9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXD9 Gene

Regulatory Elements for HOXD9 Gene

Proteins for HOXD9 Gene

  • Protein details for HOXD9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P28356-HXD9_HUMAN
    Recommended name:
    Homeobox protein Hox-D9
    Protein Accession:
    P28356
    Secondary Accessions:
    • Q86ST1

    Protein attributes for HOXD9 Gene

    Size:
    352 amino acids
    Molecular mass:
    36495 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH44855.2; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAA42016.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

neXtProt entry for HOXD9 Gene

Proteomics data for HOXD9 Gene at MOPED

Post-translational modifications for HOXD9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXD9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXD9 Gene

Domains for HOXD9 Gene

Gene Families for HOXD9 Gene

HGNC:
  • HOXL :Homeoboxes / ANTP class : HOXL subclass

UniProtKB/Swiss-Prot:

HXD9_HUMAN
Domain:
  • Contains 1 homeobox DNA-binding domain.:
    • P28356
Family:
  • Belongs to the Abd-B homeobox family.:
    • P28356
genes like me logo Genes that share domains with HOXD9: view

Function for HOXD9 Gene

Molecular function for HOXD9 Gene

GENATLAS Biochemistry: homeo box D9(4C),homologous to mouse Hox-4.4,Drosophila abd-B
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

Gene Ontology (GO) - Molecular Function for HOXD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 1756725
GO:0001227 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription IDA 1756725
GO:0003677 DNA binding --
GO:0003700 sequence-specific DNA binding transcription factor activity --
GO:0043565 sequence-specific DNA binding --
genes like me logo Genes that share ontologies with HOXD9: view
genes like me logo Genes that share phenotypes with HOXD9: view

Animal Models for HOXD9 Gene

MGI Knock Outs for HOXD9:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for HOXD9 Gene

Localization for HOXD9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXD9 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HOXD9 Gene COMPARTMENTS Subcellular localization image for HOXD9 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for HOXD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with HOXD9: view

Pathways for HOXD9 Gene

SuperPathways for HOXD9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HOXD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IDA 1756725
GO:0006351 transcription, DNA-templated IEA --
GO:0007338 single fertilization IEA --
GO:0007519 skeletal muscle tissue development IEA --
GO:0008344 adult locomotory behavior IEA --
genes like me logo Genes that share ontologies with HOXD9: view

No data available for Pathways by source for HOXD9 Gene

Compounds for HOXD9 Gene

(1) Novoseek inferred chemical compound relationships for HOXD9 Gene

Compound -log(P) Hits PubMed IDs
retinoic acid 31.9 2
genes like me logo Genes that share compounds with HOXD9: view

Transcripts for HOXD9 Gene

mRNA/cDNA for HOXD9 Gene

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

Unigene Clusters for HOXD9 Gene

Homeobox D9:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HOXD9 Gene

No ASD Table

Relevant External Links for HOXD9 Gene

GeneLoc Exon Structure for
HOXD9
ECgene alternative splicing isoforms for
HOXD9

Expression for HOXD9 Gene

mRNA expression in normal human tissues for HOXD9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXD9 Gene

This gene is overexpressed in Uterus (10.4), Vagina (5.3), Kidney - Cortex (4.6), Cervix - Ectocervix (4.5), and Colon - Sigmoid (4.4).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for HOXD9 Gene

SOURCE GeneReport for Unigene cluster for HOXD9 Gene Hs.236646

genes like me logo Genes that share expressions with HOXD9: view

Orthologs for HOXD9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HOXD9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HOXD9 36
  • 95.17 (n)
  • 93.68 (a)
HOXD9 37
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia HOXD9 36
  • 89.44 (n)
  • 88.56 (a)
HOXD9 37
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 37
  • 32 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Hoxd9 36
  • 86.19 (n)
  • 84.91 (a)
Hoxd9 16
Hoxd9 37
  • 89 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia HOXD9 37
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HOXD9 37
  • 31 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hoxd9 36
  • 87.1 (n)
  • 84.82 (a)
chicken
(Gallus gallus)
Aves HOXD9 36
  • 74.61 (n)
  • 70.86 (a)
HOXD9 37
  • 72 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 37
  • 31 (a)
ManyToMany
African clawed frog
(Xenopus laevis)
Amphibia Xl.21582 36
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxd9 36
  • 67.77 (n)
  • 63.9 (a)
zebrafish
(Danio rerio)
Actinopterygii -- 36
hoxd9a 36
  • 61.27 (n)
  • 59.92 (a)
hoxd9a 37
  • 55 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 19 (a)
OneToMany
Species with no ortholog for HOXD9:
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 HOXD9 Gene

ENSEMBL:
Gene Tree for HOXD9 (if available)
TreeFam:
Gene Tree for HOXD9 (if available)

Paralogs for HOXD9 Gene

Selected SIMAP similar genes for HOXD9 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HOXD9: view

Variants for HOXD9 Gene

Sequence variations from dbSNP and Humsavar for HOXD9 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type MAF
rs698258 -- 176,123,684(-) TAGGC(A/C/G/T)TCTAG intron-variant
rs711819 -- 176,120,968(-) ACCTC(A/G)GGTAA upstream-variant-2KB
rs711820 -- 176,122,384(-) CGGCG(A/C/G/T)GTCCA upstream-variant-2KB
rs711821 -- 176,123,287(-) GAGGC(A/C/G/T)GCCGT synonymous-codon, reference
rs711822 -- 176,124,295(-) AAAAA(A/G)AAGAA utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for HOXD9 Gene

Variant ID Type Subtype PubMed ID
dgv676n67 CNV Gain 20364138
nsv875437 CNV Loss 21882294
nsv875438 CNV Loss 21882294
nsv517968 CNV Loss 19592680
nsv875446 CNV Loss 21882294

Relevant External Links for HOXD9 Gene

HapMap Linkage Disequilibrium report
HOXD9

Disorders for HOXD9 Gene

(1) University of Copenhagen DISEASES for HOXD9 Gene

(1) Novoseek inferred disease relationships for HOXD9 Gene

Disease -log(P) Hits PubMed IDs
rheumatoid arthritis 19.6 2

Relevant External Links for HOXD9

Genetic Association Database (GAD)
HOXD9
Human Genome Epidemiology (HuGE) Navigator
HOXD9
genes like me logo Genes that share disorders with HOXD9: view

No data available for UniProtKB/Swiss-Prot for HOXD9 Gene

Publications for HOXD9 Gene

  1. HOX4 genes encode transcription factors with potential auto- and cross-regulatory capacities. (PMID: 1756725) Zappavigna V. … Duboule D. (EMBO J. 1991) 3 4 23
  2. Specificity of HOX protein function depends on DNA-protein and protein-protein interactions, both mediated by the homeo domain. (PMID: 7926763) Zappavigna V. … Mavilio F. (Genes Dev. 1994) 3 23
  3. HMG1 interacts with HOX proteins and enhances their DNA binding and transcriptional activation. (PMID: 8890171) Zappavigna V. … Bianchi M.E. (EMBO J. 1996) 3 23
  4. Immunocytochemical detection of HoxD9 and Pbx1 homeodomain protein expression in Chinese esophageal squamous cell carcinomas. (PMID: 15770739) Liu D.B. … Li J.Y. (World J. Gastroenterol. 2005) 3 23
  5. Vertebrate homeobox gene nomenclature. (PMID: 1358459) Scott M.P. (Cell 1992) 2 3

Products for HOXD9 Gene

Sources for HOXD9 Gene

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