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Aliases for HOXD9 Gene

Aliases for HOXD9 Gene

  • Homeobox D9 2 3 5
  • Homeobox Protein Hox-5.2 3 4
  • Homeobox Protein Hox-4C 3 4
  • Homeo Box D9 2 3
  • HOX4C 3 4
  • 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 HGNC Symbols for HOXD9 Gene

  • HOX4C
  • HOX4

Previous GeneCards Identifiers for HOXD9 Gene

  • GC02P175040
  • GC02P175648
  • GC02P176951
  • GC02P177189
  • GC02P176812
  • GC02P176695
  • GC02P168864
  • GC02P176987

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. Among its related pathways are Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and RNA polymerase II regulatory region sequence-specific DNA binding. An important paralog of this gene is HOXC9.

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

Additional gene information for HOXD9 Gene

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

Genomics for HOXD9 Gene

GeneHancer (GH) Regulatory Elements for HOXD9 Gene

Promoters and enhancers for HOXD9 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I176121 Promoter/Enhancer 1.1 EPDnew ENCODE 557.2 -0.1 -87 1.3 ZNF202 USF1 SUZ12 MAX USF2 POLR2A EZH2 CHD2 HOXD9 HAGLR HOXD-AS2 HOXD10
GH02I176124 Enhancer 0.5 dbSUPER 550.8 +1.9 1912 0.3 ZFHX2 ZBTB48 SUZ12 MAFK EZH2 HOXD9 GC02M176128 LOC100129455 HOXD-AS2
GH02I176128 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 15.8 +12.1 12105 13.3 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B ZNF213 E2F8 HOXD8 HOXD3 HOXD1 HAGLR ATF2 HOXD4 HOXD9 HAGLROS HOXD11 HOXD-AS2
GH02I175180 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.2 -941.4 -941438 2.2 FEZF1 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC PPARGC1A MEF2D ATP5MC3 GC02P175182 HOXD9 CIR1 HOXD4 GC02M175181
GH02I176653 Enhancer 0.9 FANTOM5 ENCODE 10.9 +531.4 531414 0.2 CTCF ZNF654 TEAD1 TRIM22 RAD21 ZNF148 GATA3 FOXK2 ZNF341 ZNF143 HOXD3 HOXD8 HOXD-AS2 HOXD9 HOXD11 LINC01116 GC02P176666 GC02P176638 LINC01117
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HOXD9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXD9 gene promoter:

Genomic Locations for HOXD9 Gene

Genomic Locations for HOXD9 Gene
chr2:176,122,685-176,124,937
(GRCh38/hg38)
Size:
2,253 bases
Orientation:
Plus strand
chr2:176,987,088-176,989,853
(GRCh37/hg19)

Genomic View for HOXD9 Gene

Genes around HOXD9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXD9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXD9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

Post-translational modifications for HOXD9 Gene

No Post-translational modifications

Other Protein References for HOXD9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXD9 Gene

Domains & Families for HOXD9 Gene

Gene Families for HOXD9 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for HOXD9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P28356

UniProtKB/Swiss-Prot:

HXD9_HUMAN :
  • Belongs to the Abd-B homeobox family.
Family:
  • Belongs to the Abd-B homeobox family.
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.

Phenotypes From GWAS Catalog for HOXD9 Gene

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 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA 1756725
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
GO:0043565 sequence-specific DNA binding IEA --
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:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HOXD9 Gene

Localization for HOXD9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXD9 Gene

Subcellular locations from

COMPARTMENTS
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 HOXD9 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HOXD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005730 nucleolus IDA --
genes like me logo Genes that share ontologies with HOXD9: view

Pathways & Interactions for HOXD9 Gene

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

Pathways by source for HOXD9 Gene

1 Cell Signaling Technology pathway for HOXD9 Gene

Gene Ontology (GO) - Biological Process for HOXD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 1756725
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0007338 single fertilization IEA --
genes like me logo Genes that share ontologies with HOXD9: view

No data available for SIGNOR curated interactions for HOXD9 Gene

Drugs & Compounds for HOXD9 Gene

(1) Additional Compounds for HOXD9 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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 :
(33) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HOXD9 Gene

Homeobox D9:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 (x10.4), Vagina (x5.3), Kidney - Cortex (x4.6), Cervix - Ectocervix (x4.5), and Colon - Sigmoid (x4.4).

Protein differential expression in normal tissues from HIPED for HOXD9 Gene

This gene is overexpressed in Pancreatic juice (56.1) and Adipocyte (10.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HOXD9 Gene



Protein tissue co-expression partners for HOXD9 Gene

NURSA nuclear receptor signaling pathways regulating expression of HOXD9 Gene:

HOXD9

SOURCE GeneReport for Unigene cluster for HOXD9 Gene:

Hs.236646

Evidence on tissue expression from TISSUES for HOXD9 Gene

  • Nervous system(4.2)
  • Intestine(4.1)
genes like me logo Genes that share expression patterns with HOXD9: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXD9 Gene

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 33 34
  • 95.17 (n)
cow
(Bos Taurus)
Mammalia HOXD9 33 34
  • 89.44 (n)
rat
(Rattus norvegicus)
Mammalia Hoxd9 33
  • 87.1 (n)
mouse
(Mus musculus)
Mammalia Hoxd9 33 16 34
  • 86.19 (n)
oppossum
(Monodelphis domestica)
Mammalia HOXD9 34
  • 69 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 34
  • 32 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia HOXD9 34
  • 31 (a)
OneToOne
chicken
(Gallus gallus)
Aves HOXD9 33 34
  • 74.61 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 31 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxd9 33
  • 67.77 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.21582 33
zebrafish
(Danio rerio)
Actinopterygii hoxd9a 33 34
  • 61.27 (n)
-- 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 19 (a)
OneToMany
Species where no ortholog for HOXD9 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)
  • 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

(9) 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 Variation AA Info Type
rs1000861220 -- 176,124,244(+) G/A 3_prime_UTR_variant
rs1001125343 -- 176,125,163(+) C/T downstream_transcript_variant
rs1002324795 -- 176,123,797(+) A/G intron_variant
rs1004285524 -- 176,123,479(+) C/A coding_sequence_variant, synonymous_variant
rs1004331389 -- 176,123,058(+) A/C coding_sequence_variant, missense_variant

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

Variant ID Type Subtype PubMed ID
nsv583673 CNV loss 21841781
nsv517968 CNV loss 19592680
dgv7173n54 CNV loss 21841781
dgv676n67 CNV gain 20364138

Variation tolerance for HOXD9 Gene

Residual Variation Intolerance Score: 58.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.60; 45.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXD9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HOXD9

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXD9 Gene

Disorders for HOXD9 Gene

MalaCards: The human disease database

(2) MalaCards diseases for HOXD9 Gene - From: GeneCards

Disorder Aliases PubMed IDs
brachydactyly-syndactyly syndrome
  • bdsd
syndactyly, type v
  • sdty5
- elite association - COSMIC cancer census association via MalaCards
Search HOXD9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for HOXD9

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HOXD9: view

No data available for UniProtKB/Swiss-Prot and Genatlas 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 (The EMBO journal 1991) 3 4 22 58
  2. Genome-wide association studies of serum magnesium, potassium, and sodium concentrations identify six Loci influencing serum magnesium levels. (PMID: 20700443) Meyer TE … Meta Analysis of Glucose and Insulin Related Traits Consortium (PLoS genetics 2010) 3 44 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. Immunocytochemical detection of HoxD9 and Pbx1 homeodomain protein expression in Chinese esophageal squamous cell carcinomas. (PMID: 15770739) Liu DB … Li JY (World journal of gastroenterology 2005) 3 22 58

Products for HOXD9 Gene

Sources for HOXD9 Gene

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