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    DLX5 distal-less homeobox 5 [ Homo sapiens (human) ]

    Gene ID: 1749, updated on 14-Nov-2024

    Summary

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    Official Symbol
    DLX5provided by HGNC
    Official Full Name
    distal-less homeobox 5provided by HGNC
    Primary source
    HGNC:HGNC:2918
    See related
    Ensembl:ENSG00000105880 MIM:600028; AllianceGenome:HGNC:2918
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SHFM1; SHFM1D
    Summary
    This gene encodes a member of a homeobox transcription factor gene family similiar to the Drosophila distal-less gene. The encoded protein may play a role in bone development and fracture healing. Mutation in this gene, which is located in a tail-to-tail configuration with another member of the family on the long arm of chromosome 7, may be associated with split-hand/split-foot malformation. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in endometrium (RPKM 4.3), placenta (RPKM 4.0) and 9 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DLX5 in Genome Data Viewer
    Location:
    7q21.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (97020396..97024831, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (98250072..98254502, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (96649708..96654143, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901703 Neighboring gene DLX6 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:96621779-96622304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:96622305-96622831 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:96627585-96628528 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:96630843-96631552 Neighboring gene VISTA enhancer hs298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18385 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:96650255-96651454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:96653649-96654365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:96655292-96655807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26299 Neighboring gene distal-less homeobox 6 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:96727665-96727870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26301 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:96763667-96763818 Neighboring gene uncharacterized LOC107984034 Neighboring gene succinate dehydrogenase complex assembly factor 3 Neighboring gene high mobility group box 3 pseudogene 21

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Sequence variants in DLX5, HOXD13 and 445 kb-microduplication surrounding BTRC cause split-hand/foot malformation in three different families.
      Title: Sequence variants in DLX5, HOXD13 and 445 kb-microduplication surrounding BTRC cause split-hand/foot malformation in three different families.
    2. Identification and functional analysis of changes to the ox-LDL-induced microRNA-124-3p/DLX5 axis in vascular smooth muscle cells.
      Title: Identification and functional analysis of changes to the ox-LDL-induced microRNA-124-3p/DLX5 axis in vascular smooth muscle cells.
    3. Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma.
      Title: Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma.
    4. Dlx5 promotes cancer progression through regulation of CCND1 in oral squamous cell carcinoma (OSCC).
      Title: Dlx5 promotes cancer progression through regulation of CCND1 in oral squamous cell carcinoma (OSCC).
    5. Inhibition of microRNA-27b-3p relieves osteoarthritis pain via regulation of KDM4B-dependent DLX5.
      Title: Inhibition of microRNA-27b-3p relieves osteoarthritis pain via regulation of KDM4B-dependent DLX5.
    6. Distal-Less Homeobox 5 Is a Therapeutic Target for Attenuating Hypertrophy and Apoptosis of Mesenchymal Progenitor Cells.
      Title: Distal-Less Homeobox 5 Is a Therapeutic Target for Attenuating Hypertrophy and Apoptosis of Mesenchymal Progenitor Cells.
    7. activation of the DLX5/KDM4B signaling pathway might serve as an intrinsic mechanism that promotes tissue regeneration mediated by dental-derived mesenchymal stem cells.
      Title: Distal-less homeobox 5 promotes the osteo-/dentinogenic differentiation potential of stem cells from apical papilla by activating histone demethylase KDM4B through a positive feedback mechanism.
    8. Inhibition of STAT5A promotes osteogenesis by DLX5 regulation.
      Title: Inhibition of STAT5A promotes osteogenesis by DLX5 regulation.
    9. Children with biobehavioral reactivity to challenge and were inhibited were found to have decreased DNA methylation of the DLX5 and IGF2 genes at both time points, as compared to non-reactive, disinhibited children.
      Title: Children's biobehavioral reactivity to challenge predicts DNA methylation in adolescence and emerging adulthood.
    10. Our data suggest that loss of DLX5, TLX1 and HOXA10 expression in late gestation is required for proper placental differentiation and function.
      Title: Increased methylation and decreased expression of homeobox genes TLX1, HOXA10 and DLX5 in human placenta are associated with trophoblast differentiation.
    Submit: New GeneRIF Correction See all GeneRIFs (42)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Split hand-foot malformation 1
    MedGen: C2931019 OMIM: 183600 GeneReviews: Not available
    		not available
    Split hand-foot malformation 1 with sensorineural hearing loss
    MedGen: C1857344 OMIM: 220600 GeneReviews: Not available
    		not available

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-05-14)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-05-14)

    ClinGen Genome Curation Page

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables HMG box domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in BMP signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in anatomical structure formation involved in morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell population proliferation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in embryonic limb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in embryonic skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endochondral ossification ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in epithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in face morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in inner ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in interneuron axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in olfactory bulb interneuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in olfactory pit development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in osteoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of epithelial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in roof of mouth development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in skeletal system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in chromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    homeobox protein DLX-5
    Names
    distal-less homeo box 5
    split hand/foot malformation type 1 with sensorineural hearing loss

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_009220.1 RefSeqGene

      Range
      5001..9436
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1279

    mRNA and Protein(s)

    1. NM_005221.6 → NP_005212.1  homeobox protein DLX-5

      See identical proteins and their annotated locations for NP_005212.1

      Status: REVIEWED

      Source sequence(s)
      BC006226, DB280023
      Consensus CDS
      CCDS5647.1
      UniProtKB/Swiss-Prot
      B7Z4P3, P56178, Q9UPL1
      UniProtKB/TrEMBL
      Q53Y73
      Related
      ENSP00000498116.1, ENST00000648378.1
      Conserved Domains (2) summary
      pfam00046
      Location:140 → 193
      Homeobox; Homeobox domain
      pfam12413
      Location:32 → 118
      DLL_N; Homeobox protein distal-less-like N terminal

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      97020396..97024831 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005250185.4 → XP_005250242.1  homeobox protein DLX-5 isoform X1

      Conserved Domains (1) summary
      pfam00046
      Location:12 → 65
      Homeobox; Homeobox domain

    2. XM_017011803.2 → XP_016867292.1  homeobox protein DLX-5 isoform X1

      Conserved Domains (1) summary
      pfam00046
      Location:12 → 65
      Homeobox; Homeobox domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      98250072..98254502 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357414.1 → XP_054213389.1  homeobox protein DLX-5 isoform X1

    2. XM_054357415.1 → XP_054213390.1  homeobox protein DLX-5 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P56178.2 GenPept UniProtKB/Swiss-Prot:P56178

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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