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    SIX5 SIX homeobox 5 [ Homo sapiens (human) ]

    Gene ID: 147912, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SIX5provided by HGNC
    Official Full Name
    SIX homeobox 5provided by HGNC
    Primary source
    HGNC:HGNC:10891
    See related
    Ensembl:ENSG00000177045 MIM:600963; AllianceGenome:HGNC:10891
    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
    BOR2; DMAHP
    Summary
    The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this gene are a cause of branchiootorenal syndrome type 2. [provided by RefSeq, Jul 2009]
    Expression
    Ubiquitous expression in ovary (RPKM 8.6), prostate (RPKM 7.4) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SIX5 in Genome Data Viewer
    Location:
    19q13.32
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (45764785..45769252, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (48592320..48596787, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (46268043..46272510, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46220214-46220884 Neighboring gene F-box protein 46 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46220885-46221555 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:46223908-46224408 Neighboring gene Sharpr-MPRA regulatory regions 3721 and 14243 Neighboring gene Sharpr-MPRA regulatory region 6016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14817 Neighboring gene meiosis initiator Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46250835-46251627 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46266800-46267354 Neighboring gene origin of replication in DMPK trinucleotide repeat region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46270229-46270864 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46270929-46271488 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14819 Neighboring gene dystrophia myotonica protein kinase repeat instability region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14820 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10797 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46274849-46275406 Neighboring gene DM1 locus antisense RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46280233-46280966 Neighboring gene DM1 protein kinase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14821 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10799 Neighboring gene DM1 locus, WD repeat containing

    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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    Related articles in PubMed

    1. Expression of a homeobox gene (SIX5) in borderline ovarian tumours. Winchester C, et al. J Clin Pathol, 2000 Mar. PMID 10823141, Free PMC Article
    2. Functional analysis of the homeodomain protein SIX5. Harris SE, et al. Nucleic Acids Res, 2000 May 1. PMID 10756185, Free PMC Article
    3. Transcription factor SIX5 is mutated in patients with branchio-oto-renal syndrome. Hoskins BE, et al. Am J Hum Genet, 2007 Apr. PMID 17357085, Free PMC Article
    4. Trinucleotide repeat expansion at the myotonic dystrophy locus reduces expression of DMAHP. Klesert TR, et al. Nat Genet, 1997 Aug. PMID 9241282
    5. Promoter of mDMAHP/Six5: differential utilization of multiple transcription initiation sites and positive/negative regulatory elements. Murakami Y, et al. Hum Mol Genet, 1998 Dec. PMID 9817928

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Phenotype-genotype correlation in patients with typical and atypical branchio-oto-renal syndrome.
      Title: Phenotype-genotype correlation in patients with typical and atypical branchio-oto-renal syndrome.
    2. the higher expressions of SIX1-5 were associated with the greater possibility of the tumorigenesis in lung neoplasms
      Title: The expression profile and clinic significance of the SIX family in non-small cell lung cancer.
    3. Three causative genes for BOR syndrome have been reported thus far: EYA1, SIX1, and SIX5, but the causative genes for approximately half of all BOR patients remain unknown.[review]
      Title: Branchio-oto-renal syndrome: comprehensive review based on nationwide surveillance in Japan.
    4. In East Asian populations, a SIX1 mutation has been reported in a Japanese family with branchio-oto (BO) syndrome,yet SIX5 mutations have never been reported.
      Title: Mutation screening of the EYA1, SIX1, and SIX5 genes in an East Asian cohort with branchio-oto-renal syndrome.
    5. Study reports a screening of 140 patients from 124 families with Branchio-oto-renal and identified 36 EYA1 mutations in 42 unrelated patients, 2 mutations, and 1 change of unknown significance in SIX1 in 3 unrelated patients, but no mutation in SIX5.
      Title: Mutation screening of the EYA1, SIX1, and SIX5 genes in a large cohort of patients harboring branchio-oto-renal syndrome calls into question the pathogenic role of SIX5 mutations.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
    7. Transcription factor SIX5 is mutated in patients with branchio-oto-renal syndrome.
      Title: Transcription factor SIX5 is mutated in patients with branchio-oto-renal syndrome.
    Submit: New GeneRIF Correction

    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
    Branchiootorenal syndrome 2
    MedGen: C1970479 OMIM: 610896 GeneReviews: Branchiootorenal Spectrum Disorder
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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 IEA
    Inferred from Electronic Annotation
    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 RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Leydig cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lens development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of skeletal muscle satellite cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spermatid development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of transcription regulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    homeobox protein SIX5
    Names
    DM locus-associated homeodomain protein
    dystrophia myotonica-associated homeodomain protein
    sine oculis homeobox homolog 5

    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_012745.2 RefSeqGene

      Range
      5000..9467
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_175875.5 → NP_787071.3  homeobox protein SIX5

      Status: REVIEWED

      Source sequence(s)
      AC074212
      Consensus CDS
      CCDS12673.1
      UniProtKB/Swiss-Prot
      Q8N196
      Related
      ENSP00000316842.4, ENST00000317578.7
      Conserved Domains (3) summary
      cd00086
      Location:206 → 257
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
      pfam16878
      Location:86 → 195
      SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain
      cl26464
      Location:424 → 663
      Atrophin-1; Atrophin-1 family

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      45764785..45769252 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      48592320..48596787 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N196.3 GenPept UniProtKB/Swiss-Prot:Q8N196

    Gene LinkOut

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

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