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    SP6 Sp6 transcription factor [ Homo sapiens (human) ]

    Gene ID: 80320, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SP6provided by HGNC
    Official Full Name
    Sp6 transcription factorprovided by HGNC
    Primary source
    HGNC:HGNC:14530
    See related
    Ensembl:ENSG00000189120 MIM:608613; AllianceGenome:HGNC:14530
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    AI1K; EPFN; KLF14; EPIPROFIN
    Summary
    SP6 belongs to a family of transcription factors that contain 3 classical zinc finger DNA-binding domains consisting of a zinc atom tetrahedrally coordinated by 2 cysteines and 2 histidines (C2H2 motif). These transcription factors bind to GC-rich sequences and related GT and CACCC boxes (Scohy et al., 2000 [PubMed 11087666]).[supplied by OMIM, Mar 2008]
    Expression
    Biased expression in placenta (RPKM 11.3), skin (RPKM 2.8) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    17q21.32
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (47844908..47876311, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48706681..48738087, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (45922274..45933063, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45907489-45908320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45908321-45909150 Neighboring gene mitochondrial ribosomal protein L10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45914101-45914648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45918111-45918666 Neighboring gene leucine rich repeat containing 46 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45924483-45925091 Neighboring gene secernin 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:45931158-45931349 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:45944035-45945234 Neighboring gene CRISPRi-validated cis-regulatory element chr17.3283 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45963041-45963574 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8643 Neighboring gene Sharpr-MPRA regulatory region 4370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8644 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:45977450-45977954 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45978459-45978962 Neighboring gene SP2 divergent transcript Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45979467-45979970 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:45981458-45981651 Neighboring gene SP2 antisense RNA 1 Neighboring gene Sp2 transcription factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46004735-46005236

    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
    • 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. Novel prostate cancer susceptibility gene SP6 predisposes patients to aggressive disease. Sipeky C, et al. Prostate Cancer Prostatic Dis, 2021 Dec. PMID 34012061, Free PMC Article
    2. A Novel De Novo SP6 Mutation Causes Severe Hypoplastic Amelogenesis Imperfecta. Kim YJ, et al. Genes (Basel), 2021 Feb 26. PMID 33652941, Free PMC Article
    3. A missense variant in specificity protein 6 (SP6) is associated with amelogenesis imperfecta. Smith CEL, et al. Hum Mol Genet, 2020 Jun 3. PMID 32167558, Free PMC Article
    4. Epiprofin orchestrates epidermal keratinocyte proliferation and differentiation. Nakamura T, et al. J Cell Sci, 2014 Dec 15. PMID 25344255, Free PMC Article
    5. The Krüppel-like factor epiprofin is expressed by epithelium of developing teeth, hair follicles, and limb buds and promotes cell proliferation. Nakamura T, et al. J Biol Chem, 2004 Jan 2. PMID 14551215

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel prostate cancer susceptibility gene SP6 predisposes patients to aggressive disease.
      Title: Novel prostate cancer susceptibility gene SP6 predisposes patients to aggressive disease.
    2. A missense variant in specificity protein 6 (SP6) is associated with amelogenesis imperfecta.
      Title: A missense variant in specificity protein 6 (SP6) is associated with amelogenesis imperfecta.
    3. A Novel De Novo SP6 Mutation Causes Severe Hypoplastic Amelogenesis Imperfecta
      Title: A Novel De Novo SP6 Mutation Causes Severe Hypoplastic Amelogenesis Imperfecta.
    4. epiprofin (Epfn, also known as Sp6) plays crucial distinct roles in these transition stages as a cell cycle regulator and a transcription factor.
      Title: Epiprofin orchestrates epidermal keratinocyte proliferation and differentiation.
    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
    Amelogenesis imperfecta, IIa 1K
    MedGen: C5774246 OMIM: 620104 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study of the rate of cognitive decline in Alzheimer's disease.
    EBI GWAS Catalog

    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

    Clone Names

    • MGC119662, MGC119663, MGC119664, MGC119665

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in epithelial to mesenchymal transition IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in odontogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of odontogenesis 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
    		  
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in cytosol 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
    transcription factor Sp6
    Names
    Kruppel-like factor 14
    krueppel-like factor 14

    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.

    mRNA and Protein(s)

    1. NM_001258248.2 → NP_001245177.1  transcription factor Sp6

      See identical proteins and their annotated locations for NP_001245177.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC003665, AK127707
      Consensus CDS
      CCDS11520.1
      UniProtKB/Swiss-Prot
      B3KXS4, Q3SY56
      UniProtKB/TrEMBL
      B3KXP2
      Related
      ENSP00000438209.1, ENST00000536300.2
      Conserved Domains (3) summary
      COG5048
      Location:261 → 336
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:259 → 278
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd22544
      Location:1 → 255
      SP6_N; N-terminal domain of transcription factor Specificity Protein (SP) 6

    2. NM_199262.3 → NP_954871.1  transcription factor Sp6

      See identical proteins and their annotated locations for NP_954871.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and represents the use of an alternate promoter, compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC003665, AK127707, AK127850
      Consensus CDS
      CCDS11520.1
      UniProtKB/Swiss-Prot
      B3KXS4, Q3SY56
      UniProtKB/TrEMBL
      B3KXP2
      Related
      ENSP00000340799.2, ENST00000342234.3
      Conserved Domains (3) summary
      COG5048
      Location:261 → 336
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:259 → 278
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd22544
      Location:1 → 255
      SP6_N; N-terminal domain of transcription factor Specificity Protein (SP) 6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      47844908..47876311 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006722115.4 → XP_006722178.1  transcription factor Sp6 isoform X1

      See identical proteins and their annotated locations for XP_006722178.1

      UniProtKB/Swiss-Prot
      B3KXS4, Q3SY56
      UniProtKB/TrEMBL
      B3KXP2
      Conserved Domains (3) summary
      COG5048
      Location:261 → 336
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:259 → 278
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd22544
      Location:1 → 255
      SP6_N; N-terminal domain of transcription factor Specificity Protein (SP) 6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      48706681..48738087 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317410.1 → XP_054173385.1  transcription factor Sp6 isoform X1

      UniProtKB/Swiss-Prot
      B3KXS4, Q3SY56
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3SY56.1 GenPept UniProtKB/Swiss-Prot:Q3SY56

    Gene LinkOut

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

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