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Aliases for HMX3 Gene

Aliases for HMX3 Gene

  • H6 Family Homeobox 3 2 3 5
  • Homeobox Protein H6 Family Member 3 3 4
  • Homeobox Protein Nkx-5.1 3 4
  • Homeo Box (H6 Family) 3 2 3
  • NKX-5.1 3 4
  • Nkx5-1 3 4
  • Homeobox (H6 Family) 3 3
  • Homeobox Protein HMX3 3
  • NKX5.1 3

External Ids for HMX3 Gene

Previous GeneCards Identifiers for HMX3 Gene

  • GC00U990140
  • GC10U900563
  • GC10P124884
  • GC10P118513

Summaries for HMX3 Gene

GeneCards Summary for HMX3 Gene

HMX3 (H6 Family Homeobox 3) is a Protein Coding gene. Diseases associated with HMX3 include Superior Semicircular Canal Dehiscence Syndrome and Semicircular Canal Dehiscence Syndrome. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HMX1.

UniProtKB/Swiss-Prot for HMX3 Gene

  • Transcription factor involved in specification of neuronal cell types and which is required for inner ear and hypothalamus development. Binds to the 5-CAAGTG-3 core sequence. Controls semicircular canal formation in the inner ear. Also required for hypothalamic/pituitary axis of the CNS (By similarity).

Additional gene information for HMX3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HMX3 Gene

Genomics for HMX3 Gene

Regulatory Elements for HMX3 Gene

Enhancers for HMX3 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
GH10H123553 1.1 FANTOM5 dbSUPER 11 +417.4 417399 0 TBL1XR1 MAX EBF1 BATF RELA POLR2A EED SMC3 ETV6 RUNX3 HMX3 LOC105378530 GC10M123502
GH10H123157 0.8 ENCODE 11.7 +21.6 21589 0 ELF3 SOX13 FOXA2 JUN CEBPG TEAD3 FOSL1 ZNF664 HIC1 POLR2A HMX3 ACADSB IKZF5 BUB3 GC10P123164
GH10H123019 0.9 ENCODE 9.9 -115.8 -115757 0 FOXA2 ATF1 ARID4B DNMT3B RARA YY1 SLC30A9 SCRT2 CREM MIXL1 ACADSB HMX3 GC10P123103
GH10H123043 0.7 ENCODE 10.7 -92.4 -92433 0 ELF3 CTCF ZNF654 BHLHE40 REST ZNF2 RAD21 CC2D1A GATA3 MBD1 ACADSB IKZF5 HMX3 GC10P123103
GH10H123550 0.5 ENCODE dbSUPER 10.8 +414.8 414778 0 HMX3 LOC105378530 GC10M123502
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HMX3 on UCSC Golden Path with GeneCards custom track

Genomic Location for HMX3 Gene

Chromosome:
10
Start:
123,135,962 bp from pter
End:
123,137,741 bp from pter
Size:
1,780 bases
Orientation:
Plus strand

Genomic View for HMX3 Gene

Genes around HMX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMX3 Gene

Proteins for HMX3 Gene

  • Protein details for HMX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A6NHT5-HMX3_HUMAN
    Recommended name:
    Homeobox protein HMX3
    Protein Accession:
    A6NHT5
    Secondary Accessions:
    • A8MU06

    Protein attributes for HMX3 Gene

    Size:
    357 amino acids
    Molecular mass:
    37825 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HMX3 Gene

Post-translational modifications for HMX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HMX3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HMX3 Gene

Domains & Families for HMX3 Gene

Gene Families for HMX3 Gene

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

Protein Domains for HMX3 Gene

Suggested Antigen Peptide Sequences for HMX3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

A6NHT5

UniProtKB/Swiss-Prot:

HMX3_HUMAN :
  • Belongs to the HMX homeobox family.
Family:
  • Belongs to the HMX homeobox family.
genes like me logo Genes that share domains with HMX3: view

Function for HMX3 Gene

Molecular function for HMX3 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor involved in specification of neuronal cell types and which is required for inner ear and hypothalamus development. Binds to the 5-CAAGTG-3 core sequence. Controls semicircular canal formation in the inner ear. Also required for hypothalamic/pituitary axis of the CNS (By similarity).

Phenotypes From GWAS Catalog for HMX3 Gene

Gene Ontology (GO) - Molecular Function for HMX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HMX3: view
genes like me logo Genes that share phenotypes with HMX3: view

Animal Models for HMX3 Gene

MGI Knock Outs for HMX3:

Animal Model Products

CRISPR Products

Transcription Factor Targets for HMX3 Gene

Selected GeneGlobe predicted Target genes for HMX3

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for HMX3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and HOMER Transcription for HMX3 Gene

Localization for HMX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMX3 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 HMX3 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Microtubule organizing center (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HMX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with HMX3: view

Pathways & Interactions for HMX3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HMX3 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:0007399 nervous system development IEA --
GO:0007420 brain development IEA --
genes like me logo Genes that share ontologies with HMX3: view

No data available for Pathways by source and SIGNOR curated interactions for HMX3 Gene

Drugs & Compounds for HMX3 Gene

No Compound Related Data Available

Transcripts for HMX3 Gene

mRNA/cDNA for HMX3 Gene

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

Unigene Clusters for HMX3 Gene

H6 family homeobox 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for HMX3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for HMX3 Gene

No ASD Table

Relevant External Links for HMX3 Gene

GeneLoc Exon Structure for
HMX3
ECgene alternative splicing isoforms for
HMX3

Expression for HMX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HMX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HMX3 Gene

This gene is overexpressed in Brain - Hypothalamus (x11.5).

Protein differential expression in normal tissues from HIPED for HMX3 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HMX3 Gene



Protein tissue co-expression partners for HMX3 Gene

NURSA nuclear receptor signaling pathways regulating expression of HMX3 Gene:

HMX3

SOURCE GeneReport for Unigene cluster for HMX3 Gene:

Hs.531194
genes like me logo Genes that share expression patterns with HMX3: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HMX3 Gene

Orthologs for HMX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for HMX3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HMX3 33
  • 99.16 (n)
dog
(Canis familiaris)
Mammalia HMX3 33 34
  • 93.19 (n)
cow
(Bos Taurus)
Mammalia HMX3 33 34
  • 91.69 (n)
mouse
(Mus musculus)
Mammalia Hmx3 33 16 34
  • 90.36 (n)
rat
(Rattus norvegicus)
Mammalia Hmx3 33
  • 90.17 (n)
oppossum
(Monodelphis domestica)
Mammalia HMX3 34
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves HMX3 33 34
  • 81.66 (n)
lizard
(Anolis carolinensis)
Reptilia HMX3 34
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hmx3 33
  • 71.72 (n)
African clawed frog
(Xenopus laevis)
Amphibia nkx-5.1-A 33
zebrafish
(Danio rerio)
Actinopterygii hmx3 33 34
  • 68.81 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2895 33
fruit fly
(Drosophila melanogaster)
Insecta Hmx 34
  • 22 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ceh-27 34
  • 22 (a)
ManyToMany
Species where no ortholog for HMX3 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)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 HMX3 Gene

ENSEMBL:
Gene Tree for HMX3 (if available)
TreeFam:
Gene Tree for HMX3 (if available)

Paralogs for HMX3 Gene

Paralogs for HMX3 Gene

(2) SIMAP similar genes for HMX3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HMX3: view

Variants for HMX3 Gene

Sequence variations from dbSNP and Humsavar for HMX3 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs1000026674 -- 123,134,107(+) TAGAT(C/G)AATGC upstream-variant-2KB
rs1000170194 -- 123,136,191(+) CCTAA(A/G)CCTCA reference, synonymous-codon
rs1000341464 -- 123,134,294(+) GAAGG(G/T)ATCCC upstream-variant-2KB
rs1000430903 -- 123,136,033(+) GGGGA(C/G)CCGGA upstream-variant-2KB
rs1002194533 -- 123,136,587(+) CTAGC(C/T)TGCCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HMX3 Gene

Variant ID Type Subtype PubMed ID
nsv1069969 CNV deletion 25765185
nsv474515 CNV novel sequence insertion 20440878

Variation tolerance for HMX3 Gene

Gene Damage Index Score: 2.96; 49.40% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HMX3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HMX3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMX3 Gene

Disorders for HMX3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for HMX3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
superior semicircular canal dehiscence syndrome
  • scds
semicircular canal dehiscence syndrome
  • scd syndrome
deafness, autosomal recessive 17
  • autosomal recessive nonsyndromic deafness 17
oculoauricular syndrome
  • ocacs
- elite association - COSMIC cancer census association via MalaCards
Search HMX3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for HMX3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HMX3
genes like me logo Genes that share disorders with HMX3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HMX3 Gene

Publications for HMX3 Gene

  1. The DNA sequence and comparative analysis of human chromosome 10. (PMID: 15164054) Deloukas P … Rogers J (Nature 2004) 3 4 60
  2. Toward a comprehensive characterization of a human cancer cell phosphoproteome. (PMID: 23186163) Zhou H … Mohammed S (Journal of proteome research 2013) 4 60
  3. Genome-wide association study of chronic periodontitis in a general German population. (PMID: 24024966) Teumer A … Kocher T (Journal of clinical periodontology 2013) 3 60
  4. Mutation analysis of Netrin 1 and HMX3 genes in patients with superior semicircular canal dehiscence syndrome. (PMID: 22779713) Roknic N … Gürtler N (Acta oto-laryngologica 2012) 3 60
  5. Mouse H6 Homeobox 1 (Hmx1) mutations cause cranial abnormalities and reduced body mass. (PMID: 19379485) Munroe RJ … Schimenti JC (BMC developmental biology 2009) 22 60

Products for HMX3 Gene

Sources for HMX3 Gene

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