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SP4 Sp4 transcription factor [ Homo sapiens (human) ]

Gene ID: 6671, updated on 18-Sep-2024

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; 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

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 
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
 

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_001326542.2NP_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: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_001326543.2NP_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:336358
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:394416
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:380403
    zf-H2C2_2; Zinc-finger double domain
    cl41773
    Location:1335
    SP1-4_N; N-terminal domain of transcription factor Specificity Proteins (SP) 1-4
  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
    O60402, Q02446, Q32M52
    Related
    ENSP00000222584.3, ENST00000222584.8
    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_137166.2 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_005249829.5XP_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_011515486.3XP_011513788.1  transcription factor Sp4 isoform X1

    Conserved Domains (3) summary
    sd00017
    Location:649671
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:677701
    zf-C2H2; Zinc finger, C2H2 type
    cd22536
    Location:32648
    SP4_N; N-terminal domain of transcription factor Specificity Protein (SP) 4
  3. XM_017012557.2XP_016868046.1  transcription factor Sp4 isoform X3

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

  5. XM_047420760.1XP_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_054358864.1XP_054214839.1  transcription factor Sp4 isoform X2

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

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

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

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