SYMPK symplekin scaffold protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYMPKprovided by HGNC
Official Full Name: symplekin scaffold proteinprovided by HGNC
Primary source: HGNC:HGNC:22935
See related: Ensembl:ENSG00000125755 MIM:602388; AllianceGenome:HGNC:22935
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: SPK; SYM; Pta1
Summary: This gene encodes a nuclear protein that functions in the regulation of polyadenylation and promotes gene expression. The protein forms a high-molecular weight complex with components of the polyadenylation machinery. It is thought to serve as a scaffold for recruiting regulatory factors to the polyadenylation complex. It also participates in 3'-end maturation of histone mRNAs, which do not undergo polyadenylation. The protein also localizes to the cytoplasmic plaques of tight junctions in some cell types. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 32.3), spleen (RPKM 15.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.32

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (45815410..45863147, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (48642851..48690585, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (46318668..46366405, complement)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The significance of nuclear symplekin in tumorigenesis is also highlighted, and ERK-dependent phosphorylation represents a mechanism for its subcellular sorting.
Title: Nuclear accumulation of symplekin promotes cellular proliferation and dedifferentiation in an ERK1/2-dependent manner.
Results indicated that reductase becomes destabilized in the absence of UBIAD1, resulting in reduced cholesterol synthesis and intracellular accumulation. Findings further establish UBIAD1 as a central player in the reductase ERAD pathway and regulation of isoprenoid synthesis.
Title: UbiA prenyltransferase domain-containing protein-1 modulates HMG-CoA reductase degradation to coordinate synthesis of sterol and nonsterol isoprenoids.
Research proved that high Rab11 expression enhances cellular multiplication and invasiveness of bladder cancer, possibly by regulating the NF-kappaB signaling pathway.
Title: Rab11 Functions as an Oncoprotein via Nuclear Factor kappa B (NF-κB) Signaling Pathway in Human Bladder Carcinoma.
Data indicate rs56848936 in the gene symplekin protein (SYMPK) at 19q13.3, associated with colon cancer risk.
Title: Novel colon cancer susceptibility variants identified from a genome-wide association study in African Americans.
CPSF2 and SYMPK, are RBFOX2 cofactors for both inclusion and exclusion of internal exons.
Title: Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors.
Symplekin interacts and co-localizes with both MOZ and MLL in immature hematopoietic cells. Its inhibition leads to a decrease of the HOXA9 protein level but not of Hoxa9 mRNA.
Title: Symplekin, a polyadenylation factor, prevents MOZ and MLL activity on HOXA9 in hematopoietic cells.
Symplekin expression regulates the assembly of tight junctions, thus helps to maintain the integrity of the epithelial monolayer and cellular polarity.
Title: Expression and distribution of symplekin regulates the assembly and function of the epithelial tight junction.
crystal structure at 2.4 A resolution of the amino-terminal domain (residues 30-340) of human symplekin in a ternary complex with the Pol II carboxy-terminal domain (CTD) Ser 5 phosphatase Ssu72 and a CTD Ser 5 phosphopeptide
Title: Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex.
Symplekin supports faithful mitosis by contributing to the formation of a bipolar spindle apparatus. Depletion of symplekin attenuates microtubule polymerization as well as expression of the critical microtubule polymerization protein CKAP5 (TOGp).
Title: Symplekin specifies mitotic fidelity by supporting microtubule dynamics.
Observational study and meta-analysis of gene-disease association. (HuGE Navigator)
Title: Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease.

Submit: New GeneRIF Correction See all GeneRIFs (15)

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

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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Markers

RH11655 (e-PCR)
- UniSTS:35107

D5S2354 (e-PCR)
- UniSTS:473392

D8S2279 (e-PCR)
- UniSTS:473907

D1S1425 (e-PCR)
- UniSTS:149621

L17877 (e-PCR)
- UniSTS:61334

L17809 (e-PCR)
- UniSTS:39087

G29025 (e-PCR)
- UniSTS:28624

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein binding	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in bicellular tight junction	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info
part_of mRNA cleavage and polyadenylation specificity factor complex	IBA Inferred from Biological aspect of Ancestor more info
located_in nuclear body	IEA Inferred from Electronic Annotation more info
located_in nuclear stress granule	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in plasma membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: symplekin

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.

mRNA and Protein(s)

NM_004819.3 → NP_004810.2 symplekin

See identical proteins and their annotated locations for NP_004810.2

Status: REVIEWED

Source sequence(s)

AC092301, BC006536, BU752018, DB044963, Y10931

Consensus CDS

CCDS12676.2

UniProtKB/Swiss-Prot

O00521, O00689, O00733, Q59GT5, Q8N2U5, Q92797

UniProtKB/TrEMBL

B7Z6F7

Related

ENSP00000245934.7, ENST00000245934.12

Conserved Domains (3) summary

pfam11935
Location:121 → 349

DUF3453; Domain of unknown function (DUF3453)

pfam12295
Location:887 → 1068

Symplekin_C; Symplekin tight junction protein C terminal

cl21453
Location:833 → 888

PKc_like; Protein Kinases, catalytic domain

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

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

45815410..45863147 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011527354.2 → XP_011525656.1 symplekin isoform X1

See identical proteins and their annotated locations for XP_011525656.1

UniProtKB/Swiss-Prot

O00521, O00689, O00733, Q59GT5, Q8N2U5, Q92797

UniProtKB/TrEMBL

B7Z6F7

Conserved Domains (3) summary

pfam11935
Location:121 → 349

DUF3453; Domain of unknown function (DUF3453)

pfam12295
Location:887 → 1068

Symplekin_C; Symplekin tight junction protein C terminal

cl21453
Location:833 → 888

PKc_like; Protein Kinases, catalytic domain
XM_047439485.1 → XP_047295441.1 symplekin isoform X2

Related

ENSP00000479480.1, ENST00000599460.5