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SP4 Sp4 transcription factor [ Homo sapiens (human) ]

Gene ID: 6671, updated on 9-Dec-2018

Summary

Official Symbol
SP4provided by HGNC
Official Full Name
Sp4 transcription factorprovided by HGNC
Primary source
HGNC:HGNC:11209
See related
Ensembl:ENSG00000105866 MIM:600540
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

Genomic context

See SP4 in Genome Data Viewer
Location:
7p15.3
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 7 NC_000007.14 (21428034..21514822)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (21467689..21554440)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene argininosuccinate synthetase 1 pseudogene 11 Neighboring gene RNA, U1 small nuclear 15, pseudogene Neighboring gene microRNA 1183 Neighboring gene uncharacterized LOC105375183 Neighboring gene dynein axonemal heavy chain 11 Neighboring gene VISTA enhancer hs294

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genetic variants at 6p21.1 and 7p15.3 are associated with risk of multiple cancers in Han Chinese.
NHGRI GWA Catalog
Genome-wide association study of recurrent early-onset major depressive disorder.
NHGRI GWA 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.
NHGRI GWA Catalog

HIV-1 interactions

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

Pathways from BioSystems

  • Endoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Endoderm Differentiation, organism-specific biosystemModel depicting endoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC130008, MGC130009

Gene Ontology Provided by GOA

Process Evidence Code Pubs
positive regulation of nucleic acid-templated transcription IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

NCBI Reference Sequences (RefSeq)

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
    5001..91789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001326542.1NP_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
    Related
    ENSP00000496957.1, ENST00000649633.1
    Conserved Domains (4) summary
    COG5048
    Location:645716
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:632654
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:690712
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:676699
    zf-H2C2_2; Zinc-finger double domain
  2. NM_001326543.1NP_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/Swiss-Prot
    Q02446
    UniProtKB/TrEMBL
    Q32M51
    Conserved Domains (3) summary
    COG5048
    Location:349420
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:336358
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:380403
    zf-H2C2_2; Zinc-finger double domain
  3. NM_003112.5NP_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
    Q02446
    Related
    ENSP00000222584.3, ENST00000222584.7
    Conserved Domains (3) summary
    sd00017
    Location:649671
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:707729
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:693716
    zf-H2C2_2; Zinc-finger double domain

RNA

  1. NR_137166.1 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)
    AK289728, BF516188

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p12 Primary Assembly

    Range
    21428034..21514822
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005249829.4XP_005249886.1  transcription factor Sp4 isoform X2

    Conserved Domains (2) summary
    sd00017
    Location:649671
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:677701
    zf-C2H2; Zinc finger, C2H2 type
  2. XM_011515486.2XP_011513788.1  transcription factor Sp4 isoform X1

    Conserved Domains (3) summary
    COG5048
    Location:662703
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:649671
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:663690
    zf-H2C2_2; Zinc-finger double domain
  3. XM_017012557.1XP_016868046.1  transcription factor Sp4 isoform X3

  4. XM_011515487.2XP_011513789.1  transcription factor Sp4 isoform X4

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