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HOXD1 Gene(Protein Coding)

Homeobox D1

GCID:
GC02P176189
GIFtS:
52
Genes Participants
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Aliases for HOXD1 Gene

Aliases for HOXD1 Gene

  • Homeobox D1 2 3 5
  • Homeobox Protein Hox-GG 3 4
  • Homeo Box D1 2 3
  • HOX4G 3 4
  • HOX4 3 4
  • Homeobox Protein Hox-D1 3
  • Homeo Box 4G 3
  • Hox-4.7 3

External Ids for HOXD1 Gene

Previous HGNC Symbols for HOXD1 Gene

  • HOX4
  • HOX4G

Previous GeneCards Identifiers for HOXD1 Gene

  • GC02P175105
  • GC02P175714
  • GC02P177017
  • GC02P177255
  • GC02P176878
  • GC02P176761
  • GC02P177053
  • GC02P168930

Summaries for HOXD1 Gene

Entrez Gene Summary for HOXD1 Gene

  • This gene is a member of the Antp homeobox family and encodes a protein with a homeobox DNA-binding domain. This nuclear protein functions as a sequence-specific transcription factor that is involved in differentiation and limb development. Mutations in this gene have been associated with severe developmental defects on the anterior-posterior (a-p) limb axis. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXD1 Gene

HOXD1 (Homeobox D1) is a Protein Coding gene. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Developmental Biology. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HOXA1.

UniProtKB/Swiss-Prot for HOXD1 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. Acts on the anterior body structures.

Gene Wiki entry for HOXD1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXD1 Gene

Genomics for HOXD1 Gene

Products:

  1. Regulatory Element

Regulatory Elements for HOXD1 Gene

Enhancers for HOXD1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G176128 1.6 Ensembl ENCODE dbSUPER 21.9 -53.8 -53790 13.3 HDGF PKNOX1 FOXA2 CREB3L1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B HOXD1 HAGLR HAGLROS HOXD4 HOXD11 ENSG00000272729 HOXD8 HOXD9 HOXD-AS2 HOXD3
GH02G176159 0.8 ENCODE 24.5 -27.4 -27366 3.0 ELF3 CTCF SUZ12 FEZF1 ZIC2 ZFHX2 EZH2 EGR2 RNF2 MTA2 HAGLROS HAGLR HOXD1 HOXD-AS2 HOXD9 HOXD3 HOXD8 HOXD10 HOXD11 HOXD13
GH02G176186 1.3 Ensembl ENCODE 13.9 -0.2 -244 2.9 HNRNPUL1 FOXA2 ATF1 ZFP64 SIN3A DMAP1 GLI4 ZNF2 ZNF48 GLIS2 HOXD1 HAGLROS
GH02G176552 1.5 FANTOM5 Ensembl ENCODE 10.2 +365.1 365112 3.0 ARNT FEZF1 ZNF2 ZBTB7B YY1 ZNF143 REST ZNF592 ATF4 SMARCA4 HOXD4 HOXD3 HOXD-AS2 MIR10B HOXD1 HAGLR HOXD13 ENSG00000236231 GC02P176590
GH02G176177 1.1 Ensembl ENCODE 12.6 -10.2 -10162 2.2 PKNOX1 FEZF1 GLIS2 ZNF366 FOS EGR2 SP3 ZNF114 ZNF579 PRDM6 HAGLROS HAGLR HOXD1 HOXD4 HOXD3 HOXD-AS2 MIR10B HOXD11 HOXD12 HOXD10
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HOXD1 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the HOXD1 gene promoter:

Genomic Location for HOXD1 Gene

Chromosome:
2
Start:
176,188,579 bp from pter
End:
176,190,907 bp from pter
Size:
2,329 bases
Orientation:
Plus strand

Genomic View for HOXD1 Gene

Genes around HOXD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXD1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HOXD1 Gene

Proteins for HOXD1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for HOXD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9GZZ0-HXD1_HUMAN
    Recommended name:
    Homeobox protein Hox-D1
    Protein Accession:
    Q9GZZ0
    Secondary Accessions:
    • B2RAB4

    Protein attributes for HOXD1 Gene

    Size:
    328 amino acids
    Molecular mass:
    34093 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HOXD1 Gene

Post-translational modifications for HOXD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for HOXD1

No data available for DME Specific Peptides for HOXD1 Gene

Domains & Families for HOXD1 Gene

Gene Families for HOXD1 Gene

HGNC:

Protein Domains for HOXD1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for HOXD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9GZZ0

UniProtKB/Swiss-Prot:

HXD1_HUMAN :
  • Belongs to the Antp homeobox family. Labial subfamily.
Family:
  • Belongs to the Antp homeobox family. Labial subfamily.
genes like me logo Genes that share domains with HOXD1: view

Function for HOXD1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for HOXD1 Gene

GENATLAS Biochemistry:
homeo box D1(4G),homologous to mouse Hox-4.9,Drosophila lab
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. Acts on the anterior body structures.

Gene Ontology (GO) - Molecular Function for HOXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXD1: view
genes like me logo Genes that share phenotypes with HOXD1: view

Animal Models for HOXD1 Gene

MGI Knock Outs for HOXD1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HOXD1 Gene

Localization for HOXD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXD1 Gene

Nucleus.

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 HOXD1 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for HOXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with HOXD1: view

Pathways & Interactions for HOXD1 Gene

genes like me logo Genes that share pathways with HOXD1: view

Gene Ontology (GO) - Biological Process for HOXD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0019233 sensory perception of pain IEA --
GO:0030182 neuron differentiation IEA --
genes like me logo Genes that share ontologies with HOXD1: view

No data available for SIGNOR curated interactions for HOXD1 Gene

Drugs & Compounds for HOXD1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for HOXD1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for HOXD1 Gene

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

Unigene Clusters for HOXD1 Gene

Homeobox D1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXD1 Gene

ExUns: 1a · 1b ^ 2 ^ 3
SP1:
SP2: -

Relevant External Links for HOXD1 Gene

GeneLoc Exon Structure for
HOXD1
ECgene alternative splicing isoforms for
HOXD1

Expression for HOXD1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXD1 Gene

mRNA expression in normal human tissues for HOXD1 Gene
mRNA expression by BioGPS for HOXD1 GenemRNA expression by GTEx for HOXD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXD1 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x10.8), Brain - Substantia nigra (x5.4), and Kidney - Cortex (x4.2).

NURSA nuclear receptor signaling pathways regulating expression of HOXD1 Gene:

HOXD1

SOURCE GeneReport for Unigene cluster for HOXD1 Gene:

Hs.83465

Evidence on tissue expression from TISSUES for HOXD1 Gene

  • Nervous system(4.4)
  • Stomach(2.3)
genes like me logo Genes that share expression patterns with HOXD1: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXD1 Gene

Orthologs for HOXD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for HOXD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia HOXD1 34 35
  • 97.87 (n)
cow
(Bos Taurus)
 Mammalia HOXD1 34 35
  • 85.71 (n)
rat
(Rattus norvegicus)
 Mammalia Hoxd1 34
  • 82.56 (n)
dog
(Canis familiaris)
 Mammalia HOXD1 34 35
  • 82.11 (n)
mouse
(Mus musculus)
 Mammalia Hoxd1 34 16 35
  • 81.95 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 35
  • 75 (a)
 OneToMany
-- 35
  • 63 (a)
 OneToMany
oppossum
(Monodelphis domestica)
 Mammalia HOXD1 35
  • 69 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia HOXD1 35
  • 34 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia hoxd1 34
  • 59.59 (n)
zebrafish
(Danio rerio)
 Actinopterygii hoxc1a 35
  • 29 (a)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta lab 35
  • 15 (a)
 OneToOne
worm
(Caenorhabditis elegans)
 Secernentea ceh-13 35
  • 31 (a)
 OneToOne
sea squirt
(Ciona savignyi)
 Ascidiacea -- 35
  • 28 (a)
 OneToOne
Species where no ortholog for HOXD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • 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)

Evolution for HOXD1 Gene

ENSEMBL:
Gene Tree for HOXD1 (if available)
TreeFam:
Gene Tree for HOXD1 (if available)

Paralogs for HOXD1 Gene

Paralogs for HOXD1 Gene

(2) SIMAP similar genes for HOXD1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with HOXD1: view

Variants for HOXD1 Gene

Sequence variations from dbSNP and Humsavar for HOXD1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1000423196 -- 176,191,128(+) ATTCT(C/T)CTGCC downstream-variant-500B
rs1001160152 -- 176,189,462(+) AGTCC(G/T)CGGGC intron-variant, upstream-variant-2KB
rs1002154023 -- 176,189,146(+) GCGTA(C/G)GACTT downstream-variant-500B, upstream-variant-2KB, reference, stop-gained
rs1003114523 -- 176,187,941(+) CACTA(C/T)AACAC intron-variant, upstream-variant-2KB
rs1003160256 -- 176,188,311(+) TCGAG(G/T)GACTA intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HOXD1 Gene

Variant ID Type Subtype PubMed ID
dgv676n67 CNV gain 20364138
nsv1001933 CNV gain 25217958

Variation tolerance for HOXD1 Gene

Residual Variation Intolerance Score: 48.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.92; 83.84% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HOXD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HOXD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXD1 Gene

Disorders for HOXD1 Gene

Relevant External Links for HOXD1

Genetic Association Database (GAD)
HOXD1
Human Genome Epidemiology (HuGE) Navigator
HOXD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HOXD1

No disorders were found for HOXD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HOXD1 Gene

Publications for HOXD1 Gene

  1. A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24. (PMID: 20852632) Goode E.L. … Pharoah P.D. (Nat. Genet. 2010) 3 46 64
  2. 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
  3. 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
  4. Isolation and characterization of the human homeobox gene HOX D1. (PMID: 11455954) Appukuttan B. … Stout J.T. (Mol. Biol. Rep. 2000) 3 4 64
  5. Vertebrate homeobox gene nomenclature. (PMID: 1358459) Scott M.P. (Cell 1992) 2 3 64

Products for HOXD1 Gene

Sources for HOXD1 Gene

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