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Aliases for HMBOX1 Gene

Aliases for HMBOX1 Gene

  • Homeobox Containing 1 2 3 5
  • Homeobox Telomere-Binding Protein 1 2 3
  • Homeobox-Containing Protein PBHNF 3
  • Homeobox-Containing Protein 1 3
  • HNF1LA 3
  • PBHNF 3
  • HOT1 3

External Ids for HMBOX1 Gene

Previous GeneCards Identifiers for HMBOX1 Gene

  • GC08P028805
  • GC08P027293

Summaries for HMBOX1 Gene

GeneCards Summary for HMBOX1 Gene

HMBOX1 (Homeobox Containing 1) is a Protein Coding gene. An important paralog of this gene is HNF1B.

UniProtKB/Swiss-Prot for HMBOX1 Gene

  • Transcription factor. Isoform 1 acts as a transcriptional repressor. Isoform 4 has very low activity as a transcriptional repressor.

Additional gene information for HMBOX1 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 HMBOX1 Gene

Genomics for HMBOX1 Gene

GeneHancer (GH) Regulatory Elements for HMBOX1 Gene

Promoters and enhancers for HMBOX1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J028888 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 -0.2 -212 4 FEZF1 DMAP1 YY1 E2F8 ZNF143 ZNF263 SP3 MEF2D GLIS1 RCOR2 HMBOX1 INTS9 KIF13B ENSG00000254129 RPL36AP32
GH08J029027 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 12.8 +138.4 138422 2.7 SRF MAFG CBFA2T3 ELF1 ZNF592 ZNF316 PRDM1 MAFK EMSY SPI1 HMBOX1 INTS9 INTS9-AS1 ENSG00000254129 KIF13B DUSP4 LOC105379346 HMBOX1-IT1
GH08J029035 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 11.3 +146.0 145974 2.1 CTCF STAT1 PKNOX1 USF1 JUN USF2 RAD21 MITF HMBOX1 ZNF143 LOC105379346 KIF13B HMBOX1 INTS9 ENSG00000254129 HMBOX1-IT1
GH08J028942 Enhancer 1.1 Ensembl ENCODE 11.4 +53.1 53092 1.3 PKNOX1 ATF1 ARNT NCOA2 TCF12 GATA2 ATF7 NCOA1 MBD2 GMEB1 HMBOX1 INTS9 ENSG00000254129 KIF13B HMBOX1-IT1 ENSG00000273710
GH08J029032 Enhancer 0.9 FANTOM5 Ensembl ENCODE dbSUPER 11.3 +142.9 142918 0.8 NR2F2 KIF13B HMBOX1 INTS9 ENSG00000254129 LOC105379346 HMBOX1-IT1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HMBOX1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HMBOX1 gene promoter:
  • AREB6
  • FOXF2
  • FOXJ2
  • HNF-3beta
  • FOXJ2 (long isoform)

Genomic Locations for HMBOX1 Gene

Genomic Locations for HMBOX1 Gene
174,546 bases
Plus strand
174,371 bases
Plus strand

Genomic View for HMBOX1 Gene

Genes around HMBOX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMBOX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMBOX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMBOX1 Gene

Proteins for HMBOX1 Gene

  • Protein details for HMBOX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox-containing protein 1
    Protein Accession:
    Secondary Accessions:
    • A4K385
    • A8K3R8
    • B4DHY5
    • D3DSU0
    • Q3Y6P1
    • Q96GS5
    • Q9H701

    Protein attributes for HMBOX1 Gene

    420 amino acids
    Molecular mass:
    47278 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAB15099.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for HMBOX1 Gene

    Alternative splice isoforms for HMBOX1 Gene


neXtProt entry for HMBOX1 Gene

Post-translational modifications for HMBOX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for HMBOX1 Gene

Domains & Families for HMBOX1 Gene

Gene Families for HMBOX1 Gene

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

Protein Domains for HMBOX1 Gene

Suggested Antigen Peptide Sequences for HMBOX1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with HMBOX1: view

No data available for UniProtKB/Swiss-Prot for HMBOX1 Gene

Function for HMBOX1 Gene

Molecular function for HMBOX1 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor. Isoform 1 acts as a transcriptional repressor. Isoform 4 has very low activity as a transcriptional repressor.

Phenotypes From GWAS Catalog for HMBOX1 Gene

Gene Ontology (GO) - Molecular Function for HMBOX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISM 19274049
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IC --
GO:0003677 DNA binding IEA --
GO:0003691 double-stranded telomeric DNA binding IDA 23685356
GO:0003720 contributes_to telomerase activity IDA 23685356
genes like me logo Genes that share ontologies with HMBOX1: view
genes like me logo Genes that share phenotypes with HMBOX1: view

Animal Model Products

CRISPR Products

miRNA for HMBOX1 Gene

miRTarBase miRNAs that target HMBOX1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMBOX1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HMBOX1 Gene

Localization for HMBOX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMBOX1 Gene

Nucleus. Cytoplasm. Note=Predominantly detected in cytoplasm. {ECO:0000269 PubMed:16825764}.
Isoform 5: Nucleus. Cytoplasm.

Subcellular locations from

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 HMBOX1 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Nuclear bodies (4)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HMBOX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000784 nuclear chromosome, telomeric region IDA 23685356
GO:0005634 nucleus IDA 19757162
GO:0005654 nucleoplasm IDA --
GO:0005697 colocalizes_with telomerase holoenzyme complex IDA 23685356
GO:0005737 cytoplasm IEA,IDA 19757162
genes like me logo Genes that share ontologies with HMBOX1: view

Pathways & Interactions for HMBOX1 Gene

SuperPathways for HMBOX1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HMBOX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 21839858
GO:0006278 RNA-dependent DNA biosynthetic process IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0032212 positive regulation of telomere maintenance via telomerase IMP 23685356
genes like me logo Genes that share ontologies with HMBOX1: view

No data available for Pathways by source and SIGNOR curated interactions for HMBOX1 Gene

Drugs & Compounds for HMBOX1 Gene

No Compound Related Data Available

Transcripts for HMBOX1 Gene

Unigene Clusters for HMBOX1 Gene

Homeobox containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMBOX1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HMBOX1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b ^ 11a · 11b · 11c
SP1: - - - - -
SP3: - - - - -
SP4: - - -
SP6: -

Relevant External Links for HMBOX1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HMBOX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HMBOX1 Gene

Protein differential expression in normal tissues from HIPED for HMBOX1 Gene

This gene is overexpressed in Urine (62.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HMBOX1 Gene

Protein tissue co-expression partners for HMBOX1 Gene

NURSA nuclear receptor signaling pathways regulating expression of HMBOX1 Gene:


SOURCE GeneReport for Unigene cluster for HMBOX1 Gene:


mRNA Expression by UniProt/SwissProt for HMBOX1 Gene:

Tissue specificity: Ubiquitous. Detected in pancreas, brain, spleen, placenta, prostate, thymus, liver, heart, bone marrow, skeletal muscle, stomach, uterus, testis, kidney, ovary, and colon.

Evidence on tissue expression from TISSUES for HMBOX1 Gene

  • Nervous system(4.3)
  • Intestine(4.2)
  • Pancreas(4.2)
genes like me logo Genes that share expression patterns with HMBOX1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for HMBOX1 Gene

Orthologs for HMBOX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for HMBOX1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HMBOX1 34 33
  • 100 (n)
(Monodelphis domestica)
Mammalia HMBOX1 34
  • 98 (a)
(Canis familiaris)
Mammalia HMBOX1 34 33
  • 96.03 (n)
(Bos Taurus)
Mammalia HMBOX1 34 33
  • 94.44 (n)
(Mus musculus)
Mammalia Hmbox1 16 34 33
  • 92.04 (n)
(Rattus norvegicus)
Mammalia Hmbox1 33
  • 91.71 (n)
(Ornithorhynchus anatinus)
Mammalia HMBOX1 34
  • 84 (a)
(Gallus gallus)
Aves HMBOX1 34 33
  • 86.4 (n)
(Anolis carolinensis)
Reptilia HMBOX1 34
  • 89 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hmbox1 33
  • 74.2 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.21282 33
(Danio rerio)
Actinopterygii hmbox1a 34
  • 71 (a)
hmbox1b 34 33
  • 70.45 (n)
HMBOX1 (3 of 3) 34
  • 48 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5873 33
(Caenorhabditis elegans)
Secernentea hmbx-1 34 33
  • 41.38 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 37 (a)
Species where no ortholog for HMBOX1 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)
  • 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 HMBOX1 Gene

Gene Tree for HMBOX1 (if available)
Gene Tree for HMBOX1 (if available)
Evolutionary constrained regions (ECRs) for HMBOX1: view image

Paralogs for HMBOX1 Gene

Paralogs for HMBOX1 Gene

(1) SIMAP similar genes for HMBOX1 Gene using alignment to 8 proteins:

genes like me logo Genes that share paralogs with HMBOX1: view

Variants for HMBOX1 Gene

Sequence variations from dbSNP and Humsavar for HMBOX1 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000005901 -- 29,057,969(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000010233 -- 28,915,253(+) TTTTTTTT/TTTTTTTTT genic_upstream_transcript_variant, intron_variant
rs1000010945 -- 29,003,754(+) TTAAATTTAAA/TTAAA intron_variant
rs1000014264 -- 28,993,341(+) A/G intron_variant
rs1000032670 -- 28,921,351(+) A/G/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HMBOX1 Gene

Variant ID Type Subtype PubMed ID
esv2661011 CNV deletion 23128226
esv2666663 CNV deletion 23128226
esv2675311 CNV deletion 23128226
esv2676816 CNV deletion 23128226
esv2736811 CNV deletion 23290073
esv2736812 CNV deletion 23290073
esv2736813 CNV deletion 23290073
esv2736814 CNV deletion 23290073
esv2736815 CNV deletion 23290073
esv3543281 CNV deletion 23714750
esv3543283 CNV deletion 23714750
esv3616751 CNV loss 21293372
esv3616752 CNV loss 21293372
esv3616753 CNV loss 21293372
esv3616754 CNV loss 21293372
esv3891379 CNV gain 25118596
nsv1030463 CNV loss 25217958
nsv1109964 CNV deletion 24896259
nsv1109965 CNV deletion 24896259
nsv1115081 CNV deletion 24896259
nsv398424 CNV insertion 16902084
nsv526818 CNV loss 19592680
nsv6136 CNV insertion 18451855
nsv820071 CNV gain 19587683

Variation tolerance for HMBOX1 Gene

Residual Variation Intolerance Score: 14.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.96; 19.88% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HMBOX1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMBOX1 Gene

Disorders for HMBOX1 Gene

Additional Disease Information for HMBOX1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for HMBOX1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HMBOX1 Gene

Publications for HMBOX1 Gene

  1. Isolation and functional analysis of human HMBOX1, a homeobox containing protein with transcriptional repressor activity. (PMID: 16825764) Chen S … Yu L (Cytogenetic and genome research 2006) 2 3 4 58
  2. Characterization of a novel human HMBOX1 splicing variant lacking the homeodomain and with attenuated transcription repressor activity. (PMID: 19757162) Zhang M … Yu L (Molecular biology reports 2010) 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for HMBOX1 Gene

Sources for HMBOX1 Gene

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