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 Syndactyly, Type V and Brachydactyly-Syndactyly Syndrome. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding 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.
No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXD9 Gene
Genomics for HOXD9 Gene
Regulatory Elements for HOXD9 Gene
Enhancers for HOXD9 Gene
- Elite enhancer and/or Elite enhancer-gene association
Download GeneHancer data dump
Enhancers around HOXD9 on UCSC Golden Path with GeneCards custom track
Regulatory Element Products
Genomic Location for HOXD9 Gene
- Chromosome:
- 2
- 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
Genes around HOXD9 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 2q31.1 by Ensembl
- 2q31.1 by Entrez Gene
- 2q31.1 by HGNC
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
- antibodies-online Antibodies for HOXD9: See all 57
- GeneTex HOXD9 antibody 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
- Origene Custom Protein Services for HOXD9
- antibodies-online Proteins for HOXD9: See all 7
- Search antibodies-online for peptides
- Search GeneTex for Proteins for HOXD9
Assay Products
No data available for DME Specific Peptides for HOXD9 Gene
Domains & Families for HOXD9 Gene
Gene Families for HOXD9 Gene
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
- 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.
| 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 binding | IDA | 1756725 |
| GO:0003677 | DNA binding | IEA | -- |
| GO:0003700 | transcription factor activity, sequence-specific DNA binding | IEA | -- |
| GO:0043565 | sequence-specific DNA binding | IEA | -- |
Phenotypes for HOXD9 Gene
- MGI mutant phenotypes for HOXD9:
- inferred from 3 alleles
- GenomeRNAi human phenotypes for HOXD9:
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
-
ViGene Biosciences lentiviral particle packaged cDNA for HOXD9 gene
-
ViGene Biosciences ready-to-package AAV shRNAs for HOXD9 gene
- Search ViGene Biosciences for HOXD9
CRISPR Products
-
OriGene CRISPR knockouts for HOXD9
-
Santa Cruz Biotechnology (SCBT) CRISPR for HOXD9
- GenScript: Design CRISPR guide RNA sequences for HOXD9
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)
miRNA Products
- Search ViGene Biosciences for HOXD9
Inhibitory RNA Products
- Origene shRNA, siRNA, and RNAi products in human, mouse, rat for HOXD9
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-
ViGene Biosciences ready-to-package AAV shRNAs for HOXD9 gene
Clone Products
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Cell Line Products
-
Horizon Cell Lines for HOXD9
-
ViGene Biosciences adenoviral particle packaged cDNA for HOXD9 gene
-
ViGene Biosciences lentiviral particle packaged cDNA for HOXD9 gene
-
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Flow Cytometry 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
- Nucleus.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005634 | nucleus | IDA | -- |
| GO:0005730 | nucleolus | IDA | -- |
Pathways & Interactions for HOXD9 Gene
No Data Available
Interacting Proteins 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:0006355 | regulation of transcription, DNA-templated | IEA | -- |
| GO:0007275 | multicellular organism development | IEA | -- |
| GO:0007338 | single fertilization | IEA | -- |
No data available for Pathways by source and 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 :
CRISPR Products
-
OriGene CRISPR knockouts for HOXD9
-
Santa Cruz Biotechnology (SCBT) CRISPR for HOXD9
- GenScript: Design CRISPR guide RNA sequences for HOXD9
miRNA Products
- Search ViGene Biosciences for HOXD9
Inhibitory RNA Products
- Origene shRNA, siRNA, and RNAi products in human, mouse, rat for HOXD9
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-
ViGene Biosciences ready-to-package AAV shRNAs for HOXD9 gene
Clone Products
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- Addgene plasmids for HOXD9
Flow Cytometry Products
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, PaxDb, 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 and template standards for HOXD9
-
OriGene qPCR primer pairs for HOXD9
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 35 |
|
||
| cow (Bos Taurus) |
Mammalia | HOXD9 34 35 |
|
||
| rat (Rattus norvegicus) |
Mammalia | Hoxd9 34 |
|
||
| mouse (Mus musculus) |
Mammalia | Hoxd9 34 16 35 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | HOXD9 35 |
|
OneToOne | |
| dog (Canis familiaris) |
Mammalia | -- 35 |
|
ManyToMany | |
| platypus (Ornithorhynchus anatinus) |
Mammalia | HOXD9 35 |
|
OneToOne | |
| chicken (Gallus gallus) |
Aves | HOXD9 34 35 |
|
||
| lizard (Anolis carolinensis) |
Reptilia | -- 35 |
|
ManyToMany | |
| tropical clawed frog (Silurana tropicalis) |
Amphibia | hoxd9 34 |
|
||
| African clawed frog (Xenopus laevis) |
Amphibia | Xl.21582 34 |
|
||
| zebrafish (Danio rerio) |
Actinopterygii | hoxd9a 34 35 |
|
||
| -- 34 |
|
||||
| sea squirt (Ciona savignyi) |
Ascidiacea | -- 35 |
|
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)
Paralogs for HOXD9 Gene
Paralogs for HOXD9 Gene
(9) SIMAP similar genes for HOXD9 Gene using alignment to 1 proteins:
Variants for HOXD9 Gene
| SNP ID | Clin | Chr 02 pos | Sequence Context | AA Info | Type |
|---|---|---|---|---|---|
| rs1000861220 | -- | 176,124,244(+) | TGTGG(A/G)TGTTT | utr-variant-3-prime | |
| rs1001125343 | -- | 176,125,163(+) | AGGTC(C/T)TCCAC | downstream-variant-500B | |
| rs1002324795 | -- | 176,123,797(+) | TTTTT(A/G)TGATA | intron-variant | |
| rs1004285524 | -- | 176,123,479(+) | ACGGG(A/C)GGCTC | reference, synonymous-codon | |
| rs1004331389 | -- | 176,123,058(+) | CTACC(A/C)CCCGT | reference, missense |
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)
Relevant External Links 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
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| syndactyly, type v |
|
|
| brachydactyly-syndactyly syndrome |
|
|
Search HOXD9 in MalaCards
View complete list of genes associated with diseases
Relevant External Links for HOXD9
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. (EMBO J. 1991) 3 4 22 64
- Genome-wide association studies of serum magnesium, potassium, and sodium concentrations identify six Loci influencing serum magnesium levels. (PMID: 20700443) Meyer T.E. … . (PLoS Genet. 2010) 3 46 64
- High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PMID: 19453261) Yerges L.M. … Zmuda J.M. (J. Bone Miner. Res. 2009) 3 46 64
- Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot. (PMID: 19938081) Ester A.R. … Hecht J.T. (Am. J. Med. Genet. A 2009) 3 46 64
- 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 22 64
Products for HOXD9 Gene
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- antibodies-online Antibodies for HOXD9: See all 57
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- ViGene Biosciences adenoviral particle packaged cDNA for HOXD9 gene
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- Mammalian expression: PiggyBac
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- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Sources for HOXD9 Gene
- (1) GeneCards
- (2) HGNC
- (3) EntrezGene
- (4) Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) GO
- (12) TrEMBL
- (13) InterPro
- (14) ProtoNet
- (15) Blocks
- (16) MGI
- (17) IUBMB
- (18) KEGG
- (19) MINT
- (20) STRING
- (21) IntAct
- (22) Novoseek
- (23) PharmGKB
- (24) DrugBank
- (25) HMDB
- (26) UniGene
- (27) AceView
- (28) RNAdb
- (29) ASD
- (30) ECgene
- (31) GeneAnnot
- (32) CGAP SAGE
- (33) SOURCE
- (34) HomoloGene
- (35) PanEnsembl
- (36) euGenes
- (37) SGD
- (38) FlyBase
- (39) WormBase
- (40) Pseudogene
- (41) DGV
- (42) dbSNP
- (43) GenAtlas
- (44) GeneTests
- (45) HGMD
- (46) GAD
- (47) LSDB
- (48) BGMUT
- (49) HuGE
- (50) eBioscience
- (51) Atlas
- (52) Cell Signaling Technology
- (53) GenBank
- (54) H-invDB
- (55) HORDE
- (56) HUGE
- (57) IMGT
- (58) Leiden
- (59) MILLIPORE
- (60) miRBase
- (61) DME
- (62) NCBI
- (63) OriGene
- (64) PubMed
- (65) R&D Systems
- (66) TGDB
- (67) Tocris
- (68) Abcam
- (69) Novus
- (70) ProSpec
- (71) Sino Biological
- (72) GenScript
- (73) Qiagen
- (74) Cloud-Clone Corp.
- (75) Enzo Life Sciences
- (76) OCA
- (77) Proteopedia
- (78) MOPED
- (79) SPIRE
- (80) neXtProt
- (81) Reactome
- (82) GeneGo (Thomson Reuters)
- (83) fRNAdb
- (84) DISEASES
- (85) SIMAP
- (86) GenomeRNAi
- (87) LifeMap
- (88) miRTarBase
- (89) MalaCards
- (90) Invitrogen
- (91) BitterDB
- (92) Vector BioLabs
- (93) ESI-BIO
- (94) RefSeq
- (95) BioSystems
- (96) MaxQB
- (97) IUPHAR
- (98) BioGPS
- (99) Illumina
- (100) COMPARTMENTS
- (101) HOMER
- (102) PaxDb
- (103) ApexBio
- (104) Addgene
- (105) antibodies-online
- (106) CYP
- (107) NONCODE
- (108) SwitchGear Genomics
- (109) TreeFam
- (110) PathCards
- (111) GeneReviews
- (112) GeneTex
- (113) Taconic Biosciences
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- (115) ProteomicsDB
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- (146) Cyagen
- (147) VectorBuilder
- (148) SNPedia
- (149) BRCA Exchange
- (150) St John's Lab
- (151) CIViC
- (152) ProteoGenix
- (153) dbSUPER
- (154) TISSUES
- (155) Gene ORGANizer