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SP9 Sp9 transcription factor [ Homo sapiens (human) ]

Gene ID: 100131390, updated on 3-Mar-2026
Official Symbol
SP9provided by HGNC
Official Full Name
Sp9 transcription factorprovided by HGNC
Primary source
HGNC:HGNC:30690
See related
Ensembl:ENSG00000217236 MIM:621003; AllianceGenome:HGNC:30690
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
ZNF990
Summary
Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. [provided by Alliance of Genome Resources, Jul 2025]
Expression
Low expression observed in reference dataset See more
Orthologs
all
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Try the new Transcripts and proteins table
See SP9 in Genome Data Viewer
Location:
2q31.1
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (174334954..174338500)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (174823644..174827190)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (175199682..175203228)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 39 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:175190859-175191676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:175193313-175194128 Neighboring gene long intergenic non-protein coding RNA 1305 Neighboring gene VISTA enhancer hs860 Neighboring gene uncharacterized LOC102724194 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12125 Neighboring gene VISTA enhancer hs953 Neighboring gene Sharpr-MPRA regulatory region 8106 Neighboring gene corepressor of RBPJ and splicing regulator Neighboring gene ReSE screen-validated silencer GRCh37_chr2:175256788-175256952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:175260886-175261386 Neighboring gene secernin 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:175274337-175274938

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. De novo variants in SP9 cause a novel form of interneuronopathy characterized by intellectual disability, autism spectrum disorder, and epilepsy with variable expressivity. Tessarech M, et al. Genet Med, 2024 May. PMID 38288683
  2. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Hillier LW, et al. Nature, 2005 Apr 7. PMID 15815621
  3. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Yin Y, et al. Science, 2017 May 5. PMID 28473536, Free PMC Article
  4. Nuclear Factor I Family Members are Key Transcription Factors Regulating Gene Expression. Malaymar Pinar D, et al. Mol Cell Proteomics, 2025 Jan. PMID 39617063, Free PMC Article
  5. A census of human transcription factors: function, expression and evolution. Vaquerizas JM, et al. Nat Rev Genet, 2009 Apr. PMID 19274049

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. De novo variants in SP9 cause a novel form of interneuronopathy characterized by intellectual disability, autism spectrum disorder, and epilepsy with variable expressivity.
    Title: De novo variants in SP9 cause a novel form of interneuronopathy characterized by intellectual disability, autism spectrum disorder, and epilepsy with variable expressivity.
Submit: New GeneRIF Correction

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

Products Interactant Other Gene Complex Source Pubs Description

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
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 sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in embryonic limb morphogenesis 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
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
transcription factor Sp9
Names
Sp9 transcription factor homolog
zinc finger protein 990

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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_001145250.2 → NP_001138722.1  transcription factor Sp9

    See identical proteins and their annotated locations for NP_001138722.1

    Status: VALIDATED

    Source sequence(s)
    AC018470
    Consensus CDS
    CCDS46453.1
    UniProtKB/Swiss-Prot
    P0CG40
    Related
    ENSP00000378418.2, ENST00000394967.3
    Conserved Domains (4) summary
    sd00017
    Location:337 → 356
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:392 → 414
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:378 → 401
    zf-H2C2_2; Zinc-finger double domain
    cd22549
    Location:19 → 333
    SP9_N; N-terminal domain of transcription factor Specificity Protein (SP) 9 and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    174334954..174338500
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    174823644..174827190
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P0CG40.1 GenPept UniProtKB/Swiss-Prot:P0CG40

Gene LinkOut

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

Chemical Information
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