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Aliases for SYMPK Gene

Aliases for SYMPK Gene

External Ids for SYMPK Gene

Previous GeneCards Identifiers for SYMPK Gene

  • GC19M050994
  • GC19M051010
  • GC19M046318
  • GC19M042747

Summaries for SYMPK Gene

Entrez Gene Summary for SYMPK Gene

  • 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]

GeneCards Summary for SYMPK Gene

SYMPK (Symplekin) is a Protein Coding gene. Among its related pathways are RNA Polymerase II Transcription Termination and Gene Expression. Gene Ontology (GO) annotations related to this gene include binding.

UniProtKB/Swiss-Prot for SYMPK Gene

  • Scaffold protein that functions as a component of a multimolecular complex involved in histone mRNA 3-end processing. Specific component of the tight junction (TJ) plaque, but might not be an exclusively junctional component. May have a house-keeping rule. Is involved in pre-mRNA polyadenylation. Enhances SSU72 phosphatase activity.

Gene Wiki entry for SYMPK Gene

Additional gene information for SYMPK Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYMPK Gene

Genomics for SYMPK Gene

GeneHancer (GH) Regulatory Elements for SYMPK Gene

Promoters and enhancers for SYMPK Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I045861 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 576.4 -1.3 -1299 5.7 MLX FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC SYMPK FOXA3 ENSG00000268810 DMWD CCDC61 CLASRP ENSG00000267114 SLC1A5 FBXO46 IRF2BP1
GH19I045763 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 37.8 +94.4 94448 10.2 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC DM1-AS SIX5 CCDC61 SYMPK FBXO46 ENSG00000268810 CLASRP ENSG00000267114 ENSG00000269148 DMWD
GH19I045690 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 39.6 +170.8 170818 3.2 HDGF FOXA2 PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B QPCTL SNRPD2 CCDC61 ENSG00000268810 SYMPK FBXO46 CLASRP ENSG00000269148 ENSG00000267114 IRF2BP1
GH19I045422 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 20.6 +438.8 438829 3.3 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 ERCC1 ZNF180 CCDC61 FBXO46 CLASRP SYMPK ENSG00000268810 ENSG00000269148 BLOC1S3 ENSG00000267114
GH19I045038 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 21 +823.2 823224 3.9 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 YBX1 YY1 POLR2B ZNF213 CLASRP ZNF180 ZNF225 ZNF284 ZNF224 MRPS15P2 ZNF223 ZNF235 ZNF234 ZNF112
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SYMPK on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SYMPK gene promoter:

Genomic Locations for SYMPK Gene

Genomic Locations for SYMPK Gene
chr19:45,815,410-45,863,290
(GRCh38/hg38)
Size:
47,881 bases
Orientation:
Minus strand
chr19:46,318,668-46,366,548
(GRCh37/hg19)

Genomic View for SYMPK Gene

Genes around SYMPK on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYMPK Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYMPK Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYMPK Gene

Proteins for SYMPK Gene

  • Protein details for SYMPK Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92797-SYMPK_HUMAN
    Recommended name:
    Symplekin
    Protein Accession:
    Q92797
    Secondary Accessions:
    • O00521
    • O00689
    • O00733
    • Q59GT5
    • Q8N2U5

    Protein attributes for SYMPK Gene

    Size:
    1274 amino acids
    Molecular mass:
    141148 Da
    Quaternary structure:
    • Found in a heat-sensitive complex at least composed of several cleavage and polyadenylation specific and cleavage stimulation factors (PubMed:16230528). Interacts with CPSF2, CPSF3 and CSTF2 (PubMed:10669729, PubMed:18688255). Interacts (via N-terminus) with HSF1; this interaction is direct and occurs upon heat shock (PubMed:14707147). Interacts with SSU72 (PubMed:20861839, PubMed:23070812).
    Miscellaneous:
    • Could be used as a differentiation marker in the differential diagnosis of tumors.
    SequenceCaution:
    • Sequence=AAC50667.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH30214.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAD92261.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=CAA71861.1; Type=Frameshift; Positions=67; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SYMPK Gene

    Alternative splice isoforms for SYMPK Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYMPK Gene

Post-translational modifications for SYMPK Gene

  • Ubiquitination at isoforms=2520, isoforms=2551, isoforms=909, isoforms=912, posLast=919919, and isoforms=1040
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SYMPK Gene

Domains & Families for SYMPK Gene

Gene Families for SYMPK Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SYMPK Gene

Suggested Antigen Peptide Sequences for SYMPK Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q92797

UniProtKB/Swiss-Prot:

SYMPK_HUMAN :
  • The HEAT repeats have been determined based on 3D-structure analysis of the D.melanogaster ortholog and are not detected by sequence-based prediction programs.
  • Belongs to the Symplekin family.
Domain:
  • The HEAT repeats have been determined based on 3D-structure analysis of the D.melanogaster ortholog and are not detected by sequence-based prediction programs.
Family:
  • Belongs to the Symplekin family.
genes like me logo Genes that share domains with SYMPK: view

Function for SYMPK Gene

Molecular function for SYMPK Gene

UniProtKB/Swiss-Prot Function:
Scaffold protein that functions as a component of a multimolecular complex involved in histone mRNA 3-end processing. Specific component of the tight junction (TJ) plaque, but might not be an exclusively junctional component. May have a house-keeping rule. Is involved in pre-mRNA polyadenylation. Enhances SSU72 phosphatase activity.

Phenotypes From GWAS Catalog for SYMPK Gene

Gene Ontology (GO) - Molecular Function for SYMPK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 14707147
genes like me logo Genes that share ontologies with SYMPK: view
genes like me logo Genes that share phenotypes with SYMPK: view

Animal Models for SYMPK Gene

MGI Knock Outs for SYMPK:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SYMPK Gene

Localization for SYMPK Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYMPK Gene

Cytoplasm, cytoskeleton. Cell junction, tight junction. Cell membrane; Peripheral membrane protein; Cytoplasmic side. Cell junction. Nucleus, nucleoplasm. Note=Cytoplasmic face of adhesion plaques (major) and nucleoplasm (minor) (in cells with TJ). Nucleoplasm (in cells without TJ). Nuclear bodies of heat-stressed cells. Colocalizes with HSF1 in nuclear stress bodies upon heat shock (PubMed:14707147). {ECO:0000269 PubMed:14707147}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYMPK gene
Compartment Confidence
plasma membrane 5
cytoskeleton 5
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Plasma membrane (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYMPK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS,IDA --
GO:0005737 cytoplasm IDA,IEA 8769423
GO:0005829 cytosol IDA --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with SYMPK: view

Pathways & Interactions for SYMPK Gene

genes like me logo Genes that share pathways with SYMPK: view

Pathways by source for SYMPK Gene

Gene Ontology (GO) - Biological Process for SYMPK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006378 mRNA polyadenylation IMP 20861839
GO:0006397 mRNA processing IEA --
GO:0006406 mRNA export from nucleus TAS --
genes like me logo Genes that share ontologies with SYMPK: view

No data available for SIGNOR curated interactions for SYMPK Gene

Drugs & Compounds for SYMPK Gene

(1) Additional Compounds for SYMPK Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SYMPK: view

Transcripts for SYMPK Gene

Unigene Clusters for SYMPK Gene

Symplekin:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYMPK Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^
SP1: - - - - -
SP2: - - - -
SP3:
SP4: -
SP5:
SP6:
SP7:
SP8: - -
SP9:
SP10:
SP11:
SP12:

ExUns: 19 ^ 20 ^ 21a · 21b ^ 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26a · 26b · 26c ^ 27 ^ 28a · 28b
SP1: - -
SP2:
SP3: - - -
SP4:
SP5: - - -
SP6: - -
SP7:
SP8:
SP9: - -
SP10:
SP11:
SP12:

Relevant External Links for SYMPK Gene

GeneLoc Exon Structure for
SYMPK
ECgene alternative splicing isoforms for
SYMPK

Expression for SYMPK Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SYMPK Gene

Protein differential expression in normal tissues from HIPED for SYMPK Gene

This gene is overexpressed in Peripheral blood mononuclear cells (13.3), Lymph node (12.6), and Bone (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SYMPK Gene



Protein tissue co-expression partners for SYMPK Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SYMPK Gene:

SYMPK

SOURCE GeneReport for Unigene cluster for SYMPK Gene:

Hs.515475

mRNA Expression by UniProt/SwissProt for SYMPK Gene:

Q92797-SYMPK_HUMAN
Tissue specificity: In testis, expressed in polar epithelia and Sertoli cells but not in vascular endothelia. The protein is detected in stomach, duodenum, pancreas, liver, fetal brain, carcinomas, lens-forming cells, fibroblasts, lymphocytes, lymphoma cells, erythroleukemia cells but not in endothelium of vessels, epidermis, intercalated disks, Purkinje fiber cells of the heart and lymph node.

Evidence on tissue expression from TISSUES for SYMPK Gene

  • Nervous system(4.9)
  • Muscle(4.5)
  • Kidney(4.3)
  • Liver(4.3)
  • Lung(4.2)
  • Intestine(2.8)
  • Blood(2.4)
genes like me logo Genes that share expression patterns with SYMPK: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYMPK Gene

Orthologs for SYMPK Gene

This gene was present in the common ancestor of animals.

Orthologs for SYMPK Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SYMPK 33 34
  • 99.58 (n)
dog
(Canis familiaris)
Mammalia SYMPK 33 34
  • 91.17 (n)
cow
(Bos Taurus)
Mammalia SYMPK 33 34
  • 90.67 (n)
mouse
(Mus musculus)
Mammalia Sympk 33 16 34
  • 87.99 (n)
oppossum
(Monodelphis domestica)
Mammalia SYMPK 34
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sympk 33
  • 86.93 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SYMPK 34
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYMPK 34
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sympk 33
  • 67.94 (n)
MGC75595 33
African clawed frog
(Xenopus laevis)
Amphibia MGC53503 33
zebrafish
(Danio rerio)
Actinopterygii si:dkeyp-117b8.1 33
  • 71.93 (n)
SYMPK 34
  • 68 (a)
OneToOne
Dr.4673 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.988 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002618 33
  • 53.05 (n)
fruit fly
(Drosophila melanogaster)
Insecta Sym 33 34
  • 47.39 (n)
worm
(Caenorhabditis elegans)
Secernentea symk-1 33 34
  • 41.53 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6518 34
  • 48 (a)
OneToOne
Species where no ortholog for SYMPK was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SYMPK Gene

ENSEMBL:
Gene Tree for SYMPK (if available)
TreeFam:
Gene Tree for SYMPK (if available)

Paralogs for SYMPK Gene

(1) SIMAP similar genes for SYMPK Gene using alignment to 8 proteins:

genes like me logo Genes that share paralogs with SYMPK: view

No data available for Paralogs for SYMPK Gene

Variants for SYMPK Gene

Sequence variations from dbSNP and Humsavar for SYMPK Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000077841 -- 45,843,031(-) T/C intron_variant
rs1000110757 -- 45,844,626(-) G/A intron_variant
rs1000146796 -- 45,821,610(-) G/C intron_variant
rs1000159962 -- 45,858,512(-) G/C intron_variant
rs1000183332 -- 45,823,096(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SYMPK Gene

Variant ID Type Subtype PubMed ID
esv25340 CNV gain 19812545
nsv1114015 CNV deletion 24896259
nsv510770 CNV deletion 20534489

Variation tolerance for SYMPK Gene

Residual Variation Intolerance Score: 1.76% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.54; 44.33% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYMPK Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYMPK

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYMPK Gene

Disorders for SYMPK Gene

Additional Disease Information for SYMPK

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SYMPK Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SYMPK Gene

Publications for SYMPK Gene

  1. Symplekin and multiple other polyadenylation factors participate in 3'-end maturation of histone mRNAs. (PMID: 16230528) Kolev NG … Steitz JA (Genes & development 2005) 3 4 22 58
  2. HSF1 modulation of Hsp70 mRNA polyadenylation via interaction with symplekin. (PMID: 14707147) Xing H … Sarge KD (The Journal of biological chemistry 2004) 3 4 22 58
  3. Complex protein interactions within the human polyadenylation machinery identify a novel component. (PMID: 10669729) Takagaki Y … Manley JL (Molecular and cellular biology 2000) 3 4 22 58
  4. Chromosomal localization to 19q13.3, partial genomic structure and 5' cDNA sequence of the human symplekin gene. (PMID: 9330635) Ueki K … Louis DN (Somatic cell and molecular genetics 1997) 2 3 4 58
  5. Symplekin, a novel type of tight junction plaque protein. (PMID: 8769423) Keon BH … Franke WW (The Journal of cell biology 1996) 3 4 22 58

Products for SYMPK Gene

Sources for SYMPK Gene

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