Aliases for HOXD9 Gene
Aliases for HOXD9 Gene
External Ids for HOXD9 Gene
- HGNC: 5140
- Entrez Gene: 3235
- Ensembl: ENSG00000128709
- OMIM: 142982
- UniProtKB: P28356
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
-
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.
Additional gene information for HOXD9 Gene
- Monarch Initiative
- Search for HOXD9 at DataMed
- Search for HOXD9 at HumanCyc
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
- Elite GeneHancer and/or Elite GeneHancer-gene association
Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)
GeneHancers around HOXD9 on UCSC Golden Path with GeneCards custom track
- Top Transcription factor binding sites by QIAGEN in the HOXD9 gene promoter:
-
- c-Ets-1
- HOXA5
- HTF
- E2F
- E2F-1
- E2F-2
- E2F-3a
- E2F-4
- AREB6
- MIF-1
Regulatory Element Products
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)
- Size:
- 2,766 bases
- Orientation:
- Plus strand
Genomic View for HOXD9 Gene
Genes around HOXD9 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 2q31.1 by Entrez Gene
- 2q31.1 by HGNC
- 2q31.1 by Ensembl
HOXD9 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene 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
- 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};
Protein Expression for HOXD9 Gene
Post-translational modifications for HOXD9 Gene
Other Protein References for HOXD9 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
- Novus Biologicals Antibodies for HOXD9
-
Abcam antibodies for HOXD9
- Invitrogen Antibodies for HOXD9 (AFLGC-HOXD9)
- GeneTex HOXD9 Antibody for HOXD9
-
Boster Bio Antibodies for HOXD9
-
Santa Cruz Biotechnology (SCBT) Antibodies for HOXD9
Protein Products
-
OriGene Purified Proteins for HOXD9
- Search Origene for MassSpec and Protein Over-expression Lysates for HOXD9
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- antibodies-online: Search results for 7 available HOXD9 Proteins ranked by validation data
- Compare Top HOXD9 Proteins
-
Quality Products:
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Assay Products
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
Protein Domains for HOXD9 Gene
Suggested Antigen Peptide Sequences for HOXD9 Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
P28356- Family:
-
- Belongs to the Abd-B homeobox family.
Function for HOXD9 Gene
Molecular function for HOXD9 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 D9(4C),homologous to mouse Hox-4.4,Drosophila abd-B
Phenotypes From GWAS Catalog 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:0000981 | RNA polymerase II transcription factor activity, sequence-specific DNA binding | NAS | 19274049 |
| 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 | -- |
Phenotypes for HOXD9 Gene
- MGI mutant phenotypes for HOXD9:
- inferred from 3 alleles
- GenomeRNAi human phenotypes for HOXD9:
Animal Models for HOXD9 Gene
Animal Model Products
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-
CRISPR Products
-
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-
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-
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miRNA for HOXD9 Gene
- miRTarBase miRNAs that target HOXD9
-
- hsa-mir-5572 (MIRT442575)
- hsa-mir-4260 (MIRT442576)
- hsa-mir-450a-2-3p (MIRT442577)
- hsa-mir-6803-5p (MIRT442578)
- hsa-mir-7109-5p (MIRT442579)
- hsa-mir-6751-5p (MIRT442580)
- hsa-mir-4665-5p (MIRT442581)
- hsa-mir-1275 (MIRT442582)
- hsa-mir-6885-5p (MIRT442583)
- hsa-mir-328-5p (MIRT442584)
- hsa-mir-6887-5p (MIRT442585)
- hsa-mir-6795-5p (MIRT442586)
- hsa-mir-625-5p (MIRT442587)
- hsa-mir-4786-3p (MIRT442588)
- hsa-mir-551b-5p (MIRT442589)
- hsa-mir-2355-5p (MIRT536749)
- hsa-mir-454-5p (MIRT536750)
- hsa-mir-488-5p (MIRT536751)
- hsa-mir-6776-3p (MIRT536752)
- hsa-mir-4715-3p (MIRT715089)
- hsa-mir-4727-5p (MIRT715090)
- hsa-mir-4713-3p (MIRT715091)
- hsa-mir-6817-5p (MIRT715092)
- hsa-mir-4769-3p (MIRT715093)
- hsa-mir-6728-3p (MIRT715094)
- hsa-mir-361-3p (MIRT715095)
- hsa-mir-3156-5p (MIRT715096)
- hsa-mir-29b-2-5p (MIRT724682)
- hsa-mir-3614-5p (MIRT724683)
- hsa-mir-1179 (MIRT761183)
- hsa-mir-4436b-5p (MIRT769120)
- hsa-mir-6509-3p (MIRT776631)
- hsa-mir-7158-3p (MIRT781565)
miRNA Products
Inhibitory RNA Products
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Clone Products
- Sino Biological Human cDNA Clone for HOXD9
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- Applied Biological Materials Clones for HOXD9
-
Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
Cell Line Products
-
Horizon Cell Lines for HOXD9
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
- Nucleus.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
- Nucleoli (3)
- Nucleus (3)
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005634 | nucleus | IDA | -- |
| GO:0005730 | nucleolus | IDA | -- |
Pathways & Interactions for HOXD9 Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | Chromatin Regulation / Acetylation | ||
Pathways by source for HOXD9 Gene
1 Cell Signaling Technology pathway for HOXD9 Gene
Interacting Proteins for HOXD9 Gene
GPS-Prot Interaction Network for HOXD9
| 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 | -- |
No data available for SIGNOR curated interactions for HOXD9 Gene
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 :
-
- ENST00000249499 1870 bps (uc010zex.3)
CRISPR Products
-
OriGene CRISPR knockouts for HOXD9
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-
Vectors and viruses for KO, Activation, Repression, and more
-
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- GenScript: Design CRISPR guide RNA sequences for HOXD9
miRNA Products
Inhibitory RNA Products
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Clone Products
- Sino Biological Human cDNA Clone for HOXD9
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-
Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
Expression for HOXD9 Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
-
Limb (Muscoskeletal System)
- Progress Zone Cells Limb Bud
- Prechondrocytic Mesenchymal Cells Zeugopod
- Limb Bud Mesenchyme Cells Limb Bud
- Autopod
- Stylopod
-
Bone (Muscoskeletal System)
- Osteochondro Mesenchymal Cells Rib
- Sclerotome Cells Lumbar Mesenchymal Sclerotome
- Progress Zone Cells Limb Bud
- Prechondrocytic Mesenchymal Cells Zeugopod
-
Cartilage (Muscoskeletal System)
- Osteochondro Mesenchymal Cells Rib
- Sclerotome Cells Lumbar Mesenchymal Sclerotome
- Progress Zone Cells Limb Bud
- Prechondrocytic Mesenchymal Cells Zeugopod
-
Somite (Muscoskeletal System)
- Sclerotome Cells Lumbar Mesenchymal Sclerotome
-
Tendon amp Ligament
- Sclerotome Cells Lumbar Mesenchymal Sclerotome
-
Mesoderm (Gastrulation Derivatives)
- Limb Bud Mesenchyme Cells Limb Bud
- Gut Tube (Gastrointestinal Tract)
- Lower Urinary Tract (Urinary System)
- Kidney (Urinary System)
- Heart (Cardiovascular System)
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).
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 and MOPED for HOXD9 Gene
NURSA nuclear receptor signaling pathways regulating expression of HOXD9 Gene:
HOXD9SOURCE GeneReport for Unigene cluster for HOXD9 Gene:
Hs.236646Evidence on tissue expression from TISSUES for HOXD9 Gene
- Nervous system(4.2)
- Intestine(4.1)
Primer Products
-
OriGene qPCR primer pairs for HOXD9
-
OriGene qPCR primer pairs and template standards for HOXD9
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Gene Expression Assay 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.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | HOXD9 34 33 |
|
OneToOne | |
| cow (Bos Taurus) |
Mammalia | HOXD9 34 33 |
|
OneToOne | |
| rat (Rattus norvegicus) |
Mammalia | Hoxd9 33 |
|
||
| mouse (Mus musculus) |
Mammalia | Hoxd9 16 34 33 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | HOXD9 34 |
|
OneToOne | |
| dog (Canis familiaris) |
Mammalia | -- 34 |
|
ManyToMany | |
| platypus (Ornithorhynchus anatinus) |
Mammalia | HOXD9 34 |
|
OneToOne | |
| chicken (Gallus gallus) |
Aves | HOXD9 34 33 |
|
OneToOne | |
| lizard (Anolis carolinensis) |
Reptilia | -- 34 |
|
ManyToMany | |
| tropical clawed frog (Silurana tropicalis) |
Amphibia | hoxd9 33 |
|
||
| African clawed frog (Xenopus laevis) |
Amphibia | Xl.21582 33 |
|
||
| zebrafish (Danio rerio) |
Actinopterygii | hoxd9a 34 33 |
|
OneToOne | |
| -- 33 |
|
||||
| sea squirt (Ciona savignyi) |
Ascidiacea | -- 34 |
|
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)
- Aminode:
- Evolutionary constrained regions (ECRs) for HOXD9: view image
Paralogs for HOXD9 Gene
Paralogs for HOXD9 Gene
(9) SIMAP similar genes for HOXD9 Gene using alignment to 1 proteins:
- HXD9_HUMAN
Variants 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 |
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
SNP Genotyping and Copy Number Assay Products
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXD9 Gene
Disorders for HOXD9 Gene
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| brachydactyly-syndactyly syndrome |
|
|
| syndactyly, type v |
|
|
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
No data available for UniProtKB/Swiss-Prot and Genatlas for HOXD9 Gene
Publications for HOXD9 Gene
- 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
- 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
- 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
- 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
- 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
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Sources for HOXD9 Gene
- (1) GeneCards
- (2) HGNC
- (3) EntrezGene
- (4) Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
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