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SP6 Sp6 transcription factor [ Homo sapiens (human) ]

Gene ID: 80320, updated on 2-Nov-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
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Genomic context

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See SP6 in Genome Data Viewer
Location:
17q21.32
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (47844908..47876311, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48706681..48738087, complement)
RS_2024_09 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 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
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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
located_in 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_2024_08

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

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