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    SP4 Sp4 transcription factor [ Homo sapiens (human) ]

    Gene ID: 6671, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SP4provided by HGNC
    Official Full Name
    Sp4 transcription factorprovided by HGNC
    Primary source
    HGNC:HGNC:11209
    See related
    Ensembl:ENSG00000105866 MIM:600540; AllianceGenome:HGNC:11209
    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
    HF1B; SPR-1
    Summary
    The protein encoded by this gene is a transcription factor that can bind to the GC promoter region of a variety of genes, including those of the photoreceptor signal transduction system. The encoded protein binds to the same sites in promoter CpG islands as does the transcription factor SP1, although its expression is much more restricted compared to that of SP1. This gene may be involved in bipolar disorder and schizophrenia. [provided by RefSeq, May 2016]
    Expression
    Ubiquitous expression in ovary (RPKM 3.6), thyroid (RPKM 3.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SP4 in Genome Data Viewer
    Location:
    7p15.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (21428083..21514822)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (21564221..21650967)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (21467701..21554440)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:21300935-21301660 Neighboring gene argininosuccinate synthetase 1 pseudogene 11 Neighboring gene NANOG hESC enhancer GRCh37_chr7:21320731-21321232 Neighboring gene MPRA-validated peak6423 silencer Neighboring gene MPRA-validated peak6424 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25695 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25696 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25697 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25698 Neighboring gene MPRA-validated peak6425 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25699 Neighboring gene RNA, U1 small nuclear 15, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17996 Neighboring gene Sharpr-MPRA regulatory region 5184 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:21520156-21520779 Neighboring gene microRNA 1183 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:21581979-21582480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17997 Neighboring gene NANOG hESC enhancer GRCh37_chr7:21584813-21585779 Neighboring gene uncharacterized LOC105375183 Neighboring gene dynein axonemal heavy chain 11 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:21639662-21640861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25700 Neighboring gene NANOG hESC enhancer GRCh37_chr7:21804820-21805335 Neighboring gene VISTA enhancer hs294 Neighboring gene uncharacterized LOC124901599

    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. Common and rare variants within SP4 exert distinct molecular mechanisms contributing to the risk of schizophrenia. Zhang Q, et al. Psychiatry Res, 2022 Dec. PMID 36372009
    2. The genetic polymorphisms in the SP4 gene and the risk of gastric cancer. Cui Y, et al. Future Oncol, 2022 Nov. PMID 36346067
    3. Over-representation of potential SP4 target genes within schizophrenia-risk genes. Zhou X. Mol Psychiatry, 2022 Feb. PMID 34750502, Free PMC Article
    4. Human Sp4 transcription factor gene (SP4) maps to chromosome 7p15. Kalff-Suske M, et al. Genomics, 1995 Apr 10. PMID 7607696
    5. Phosphorylation of transcription factor specificity protein 4 is increased in peripheral blood mononuclear cells of first-episode psychosis. Pinacho R, et al. PLoS One, 2015. PMID 25915526, Free PMC Article

    See all (61) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SP4 Facilitates Esophageal Squamous Cell Carcinoma Progression by Activating PHF14 Transcription and Wnt/Beta-Catenin Signaling.
      Title: SP4 Facilitates Esophageal Squamous Cell Carcinoma Progression by Activating PHF14 Transcription and Wnt/Β-Catenin Signaling.
    2. The FOXP4-AS1/miR-3130-3p/SP4 feedback loop is associated with prostate cancer.
      Title: The FOXP4-AS1/miR-3130-3p/SP4 feedback loop is associated with prostate cancer.
    3. Common and rare variants within SP4 exert distinct molecular mechanisms contributing to the risk of schizophrenia.
      Title: Common and rare variants within SP4 exert distinct molecular mechanisms contributing to the risk of schizophrenia.
    4. The genetic polymorphisms in the SP4 gene and the risk of gastric cancer.
      Title: The genetic polymorphisms in the SP4 gene and the risk of gastric cancer.
    5. Sp4 Regulates PTTG1IP Gene Transcription and Expression.
      Title: Sp4 Regulates PTTG1IP Gene Transcription and Expression.
    6. Over-representation of potential SP4 target genes within schizophrenia-risk genes.
      Title: Over-representation of potential SP4 target genes within schizophrenia-risk genes.
    7. Sp1, Sp3 and Sp4 are non-oncogene addiction (NOA) genes and are attractive drug targets for individual and combined cancer chemotherapies.
      Title: Specificity protein (Sp) transcription factors Sp1, Sp3 and Sp4 are non-oncogene addiction genes in cancer cells.
    8. Common risk factors in the SP4 gene are associated with schizophrenia, although not with MDD, in the Han Chinese population.
      Title: Role played by the SP4 gene in schizophrenia and major depressive disorder in the Han Chinese population.
    9. IN TMD patients, a novel locus at genome-wide level of significance (rs73460075, OR = 0.56, P = 3.8 x 10(-8)) in the intron of the dystrophin gene DMD (X chromosome), and a suggestive locus on chromosome 7 (rs73271865, P = 2.9 x 10(-7)) upstream of the Sp4 Transcription Factor ( SP4) gene were identified in the discovery cohort, but neither of these was replicated.
      Title: GWAS Identifies New Loci for Painful Temporomandibular Disorder: Hispanic Community Health Study/Study of Latinos.
    10. Results indicate that SP4 S770 phosphorylation is increased in the cerebellum in bipolar disorder that committed suicide and in severe schizophrenia, and may be part of a degradation signal that controls Sp4 abundance in cerebellar granule neurons
      Title: Transcription factor SP4 phosphorylation is altered in the postmortem cerebellum of bipolar disorder and schizophrenia subjects.
    Submit: New GeneRIF Correction See all GeneRIFs (32)

    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

    EBI GWAS Catalog

    Description
    Genetic variants at 6p21.1 and 7p15.3 are associated with risk of multiple cancers in Han Chinese.
    EBI GWAS Catalog
    Genome-wide association study of recurrent early-onset major depressive disorder.
    EBI GWAS Catalog
    Novel loci for major depression identified by genome-wide association study of Sequenced Treatment Alternatives to Relieve Depression and meta-analysis of three studies.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Sp4 is an activator of the HIV-1 LTR promoter, suggesting an indirect interaction to enhance HIV-1 Tat-mediated transactivation of the viral promoter PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC130008, MGC130009

    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 identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within_positive_effect regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    transcription factor Sp4

    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_050737.1 RefSeqGene

      Range
      5050..91789
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001326542.2 → NP_001313471.1  transcription factor Sp4 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction in the 5' end compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AC004595, BF438799
      Consensus CDS
      CCDS94063.1
      UniProtKB/TrEMBL
      A0A3B3IRW4
      Related
      ENSP00000496957.1, ENST00000649633.1
      Conserved Domains (4) summary
      COG5048
      Location:645 → 716
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:632 → 654
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:690 → 712
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:676 → 699
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001326543.2 → NP_001313472.1  transcription factor Sp4 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice junction in the 5' end compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AC004595, AK289728, BC109301, BF438799
      UniProtKB/TrEMBL
      Q32M51
      Conserved Domains (4) summary
      sd00017
      Location:336 → 358
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:394 → 416
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:380 → 403
      zf-H2C2_2; Zinc-finger double domain
      cl41773
      Location:1 → 335
      SP1-4_N; N-terminal domain of transcription factor Specificity Proteins (SP) 1-4

    3. NM_003112.5 → NP_003103.2  transcription factor Sp4 isoform 1

      See identical proteins and their annotated locations for NP_003103.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC004595, AK289728, BF438799
      Consensus CDS
      CCDS5373.1
      UniProtKB/Swiss-Prot
      O60402, Q02446, Q32M52
      Related
      ENSP00000222584.3, ENST00000222584.8
      Conserved Domains (3) summary
      sd00017
      Location:649 → 671
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:707 → 729
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:693 → 716
      zf-H2C2_2; Zinc-finger double domain

    RNA

    1. NR_137166.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 3' end compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AC004595, AK289728, BF516188

    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
      21428083..21514822
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005249829.5 → XP_005249886.1  transcription factor Sp4 isoform X2

      Conserved Domains (2) summary
      sd00017
      Location:649 → 671
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:677 → 701
      zf-C2H2; Zinc finger, C2H2 type

    2. XM_011515486.3 → XP_011513788.1  transcription factor Sp4 isoform X1

      Conserved Domains (3) summary
      sd00017
      Location:649 → 671
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:677 → 701
      zf-C2H2; Zinc finger, C2H2 type
      cd22536
      Location:32 → 648
      SP4_N; N-terminal domain of transcription factor Specificity Protein (SP) 4

    3. XM_017012557.2 → XP_016868046.1  transcription factor Sp4 isoform X3

    4. XM_011515487.3 → XP_011513789.1  transcription factor Sp4 isoform X4

    5. XM_047420760.1 → XP_047276716.1  transcription factor Sp4 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      21564221..21650967
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358864.1 → XP_054214839.1  transcription factor Sp4 isoform X2

    2. XM_054358863.1 → XP_054214838.1  transcription factor Sp4 isoform X1

    3. XM_054358865.1 → XP_054214840.1  transcription factor Sp4 isoform X3

    4. XM_054358866.1 → XP_054214841.1  transcription factor Sp4 isoform X4

    5. XM_054358867.1 → XP_054214842.1  transcription factor Sp4 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q02446.2 GenPept UniProtKB/Swiss-Prot:Q02446

    Gene LinkOut

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

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