SNAPC4 small nuclear RNA activating complex polypeptide 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SNAPC4provided by HGNC
Official Full Name: small nuclear RNA activating complex polypeptide 4provided by HGNC
Primary source: HGNC:HGNC:11137
See related: Ensembl:ENSG00000165684 MIM:602777; AllianceGenome:HGNC:11137
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: NEDRSO; SNAP190; PTFalpha
Summary: This gene encodes the largest subunit of the small nuclear RNA-activating protein (SNAP) complex. The encoded protein contains a Myb DNA-binding domain, and is essential for RNA polymerase II and III polymerase transcription from small nuclear RNA promoters. A mutation in this gene is associated with ankylosing spondylitis. [provided by RefSeq, Jul 2016]
Expression: Broad expression in testis (RPKM 5.9), spleen (RPKM 2.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q34.3

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (136375571..136400170, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (148604905..148629504, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (139270023..139294622, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Bi-allelic SNAPC4 variants dysregulate global alternative splicing and lead to neuroregression and progressive spastic paraparesis.
Title: Bi-allelic SNAPC4 variants dysregulate global alternative splicing and lead to neuroregression and progressive spastic paraparesis.
Report no significant association between SNAPC4 SNPs and ankylosing spondylitis.
Title: Determination of IL1 R2, ANTXR2, CARD9, and SNAPC4 single nucleotide polymorphisms in Iranian patients with ankylosing spondylitis.
Our study confirmed that an SNP rs11145835 in 9q34.3 that harbors CARD9 and SNAPC4 is associated with ankylosing spondylitis in a Chinese Han population
Title: Evidence for genetic association of CARD9 and SNAPC4 with ankylosing spondylitis in a Chinese Han population.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study of gene-disease association. (HuGE Navigator)
Title: Elucidating the chromosome 9 association with AS; CARD9 is a candidate gene.
CK2 phosphorylation triggers an allosteric inhibition of the SNAP190 Myb DNA binding domain
Title: The protein kinase CK2 phosphorylates SNAP190 to negatively regulate SNAPC DNA binding and human U6 transcription by RNA polymerase III.
CK2 may have the capacity to differentially regulate U1 and U6 transcription even though SNAP(C) is universally utilized for human snRNA gene transcription [SNAPC protein, also called PTF or PSE-binding transcription factor]
Title: Cooperation between small nuclear RNA-activating protein complex (SNAPC) and TATA-box-binding protein antagonizes protein kinase CK2 inhibition of DNA binding by SNAPC.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neurodevelopmental disorder with motor regression, progressive spastic paraplegia, and oromotor dysfunction MedGen: C5882695 OMIM: 620515 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II general transcription initiation factor activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase III general transcription initiation factor activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase III type 3 promoter sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in snRNA transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in snRNA transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in snRNA transcription by RNA polymerase III	IBA Inferred from Biological aspect of Ancestor more info
involved_in snRNA transcription by RNA polymerase III	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IC Inferred by Curator more info	PubMed
part_of snRNA-activating protein complex	IBA Inferred from Biological aspect of Ancestor more info
part_of snRNA-activating protein complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: snRNA-activating protein complex subunit 4

Names: PSE-binding factor subunit alpha; PTF subunit alpha; SNAPc 190 kDa subunit; SNAPc subunit 4; proximal sequence element-binding transcription factor subunit alpha; snRNA-activating protein complex 190 kDa subunit

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

NG_051233.1 RefSeqGene

Range

5051..29650

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001394201.1 → NP_001381130.1 snRNA-activating protein complex subunit 4 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AL592301

Consensus CDS

CCDS6998.1

UniProtKB/Swiss-Prot

Q5SXM2, Q9Y6P7

Related

ENSP00000490037.2, ENST00000637388.2

Conserved Domains (5) summary

smart00717
Location:401 → 448

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

PLN03091
Location:399 → 502

PLN03091; hypothetical protein; Provisional

PHA03247
Location:817 → 1215

PHA03247; large tegument protein UL36; Provisional

pfam13921
Location:297 → 357

Myb_DNA-bind_6; Myb-like DNA-binding domain

cl21498
Location:262 → 305

SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
NM_001394202.1 → NP_001381131.1 snRNA-activating protein complex subunit 4 isoform b

Status: REVIEWED

Source sequence(s)

AL592301

Conserved Domains (5) summary

smart00717
Location:401 → 448

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

PLN03091
Location:399 → 502

PLN03091; hypothetical protein; Provisional

PHA03247
Location:789 → 1187

PHA03247; large tegument protein UL36; Provisional

pfam13921
Location:297 → 357

Myb_DNA-bind_6; Myb-like DNA-binding domain

cl21498
Location:262 → 305

SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
NM_001394203.1 → NP_001381132.1 snRNA-activating protein complex subunit 4 isoform b

Status: REVIEWED

Source sequence(s)

AL592301

Conserved Domains (5) summary

smart00717
Location:401 → 448

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

PLN03091
Location:399 → 502

PLN03091; hypothetical protein; Provisional

PHA03247
Location:789 → 1187

PHA03247; large tegument protein UL36; Provisional

pfam13921
Location:297 → 357

Myb_DNA-bind_6; Myb-like DNA-binding domain

cl21498
Location:262 → 305

SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
NM_003086.4 → NP_003077.2 snRNA-activating protein complex subunit 4 isoform a

See identical proteins and their annotated locations for NP_003077.2

Status: REVIEWED

Source sequence(s)

AL592301

Consensus CDS

CCDS6998.1

UniProtKB/Swiss-Prot

Q5SXM2, Q9Y6P7

Related

ENSP00000510559.1, ENST00000684778.1

Conserved Domains (5) summary

smart00717
Location:401 → 448

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

PLN03091
Location:399 → 502

PLN03091; hypothetical protein; Provisional

PHA03247
Location:817 → 1215

PHA03247; large tegument protein UL36; Provisional

pfam13921
Location:297 → 357

Myb_DNA-bind_6; Myb-like DNA-binding domain

cl21498
Location:262 → 305

SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

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

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

136375571..136400170 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047423780.1 → XP_047279736.1 snRNA-activating protein complex subunit 4 isoform X2
XM_006717242.5 → XP_006717305.1 snRNA-activating protein complex subunit 4 isoform X1

See identical proteins and their annotated locations for XP_006717305.1

UniProtKB/Swiss-Prot

Q5SXM2, Q9Y6P7

Conserved Domains (5) summary

smart00717
Location:401 → 448

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

PLN03091
Location:399 → 502

PLN03091; hypothetical protein; Provisional

PHA03247
Location:817 → 1215

PHA03247; large tegument protein UL36; Provisional

pfam13921
Location:297 → 357

Myb_DNA-bind_6; Myb-like DNA-binding domain

cl21498
Location:262 → 305

SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
XM_006717244.3 → XP_006717307.1 snRNA-activating protein complex subunit 4 isoform X4

Conserved Domains (1) summary

PHA03247
Location:221 → 619

PHA03247; large tegument protein UL36; Provisional
XM_047423781.1 → XP_047279737.1 snRNA-activating protein complex subunit 4 isoform X3
XM_047423782.1 → XP_047279738.1 snRNA-activating protein complex subunit 4 isoform X5

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

148604905..148629504 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054363624.1 → XP_054219599.1 snRNA-activating protein complex subunit 4 isoform X2
XM_054363623.1 → XP_054219598.1 snRNA-activating protein complex subunit 4 isoform X1
XM_054363626.1 → XP_054219601.1 snRNA-activating protein complex subunit 4 isoform X4
XM_054363625.1 → XP_054219600.1 snRNA-activating protein complex subunit 4 isoform X3
XM_054363627.1 → XP_054219602.1 snRNA-activating protein complex subunit 4 isoform X5