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SP4 Sp4 transcription factor [ Homo sapiens (human) ]

Gene ID: 6671, updated on 23-Nov-2023

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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (21428083..21514822)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (21564221..21650967)
105.20220307 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
  • 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. Role played by the SP4 gene in schizophrenia and major depressive disorder in the Han Chinese population. Chen J, et al. Br J Psychiatry, 2016 May. PMID 26450579
  5. Transcription factor SP4 phosphorylation is altered in the postmortem cerebellum of bipolar disorder and schizophrenia subjects. Pinacho R, et al. Eur Neuropsychopharmacol, 2015 Oct. PMID 26049820, Free PMC Article

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. Sp4 Regulates PTTG1IP Gene Transcription and Expression.
    Title: Sp4 Regulates PTTG1IP Gene Transcription and Expression.
  5. Over-representation of potential SP4 target genes within schizophrenia-risk genes.
    Title: Over-representation of potential SP4 target genes within schizophrenia-risk genes.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. O-GlcNAc modification of Sp3 and Sp4, but not Sp2 transcription factors negatively regulates their transcriptional activities.
    Title: O-GlcNAc modification of Sp3 and Sp4 transcription factors negatively regulates their transcriptional activities.
Submit: New GeneRIF Correction See all GeneRIFs (31)

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
part_of 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_2023_10

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

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