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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. Diseases associated with SYMPK include Vein Disease. Among its related pathways are Sertoli-Sertoli Cell Junction Dynamics and Gene Expression. 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

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

Genomics for SYMPK Gene

Regulatory Elements for SYMPK Gene

Enhancers for SYMPK Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19G045763 1.7 Ensembl ENCODE dbSUPER 18.8 +94.4 94449 10.2 MLX CREB3L1 AGO1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC FBXO46 SYMPK DMWD CCDC61 ENSG00000269148 DMPK BHMG1 FOXA3 ENSG00000266958 PRKD2
GH19G045861 1.7 Ensembl ENCODE dbSUPER 13.9 -1.3 -1299 5.7 MLX CREB3L1 FEZF1 DMAP1 YY1 ZNF143 SP3 NFYC TBX21 ZNF610 ENSG00000268810 DMWD SYMPK SLC1A5 IRF2BP1 MYPOP RELB ENSG00000267114 DMPK CLASRP
GH19G045999 1.5 FANTOM5 Ensembl ENCODE 11 -137.2 -137153 1.7 ATF1 ZNF2 GLIS2 ZNF548 SP3 YY2 NCOA1 TSHZ1 ZNF518A ZNF610 CCDC61 FOXA3 SYMPK ENSG00000268810 PNMA8A EML2 PNMA8B NOVA2 GC19M045998
GH19G045809 1.2 Ensembl ENCODE 13.3 +53.1 53129 1.6 HDGF CBX3 ARNT NFRKB ZNF121 ZNF350 FOS EGR2 ZNF174 CEBPB DMWD SYMPK CCDC61 IRF2BP1 DMPK PIR50651 GC19M045805 RSPH6A
GH19G046077 1.5 Ensembl ENCODE dbSUPER 10 -214.4 -214430 0.6 ARID4B SIN3A ZNF2 GLIS2 ZNF143 FOS YY2 REST MIER2 KAT8 IGFL3 HIF3A FOXA3 SYMPK LOC400706 GC19P046077
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SYMPK on UCSC Golden Path with GeneCards custom track

Promoters for SYMPK Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000288680 290 1601 HDGF PKNOX1 MLX CREB3L1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for SYMPK Gene

Chromosome:
19
Start:
45,815,410 bp from pter
End:
45,863,290 bp from pter
Size:
47,881 bases
Orientation:
Minus strand

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 Lys520, isoforms=2551, Lys909, isoforms=912, Lys919, and posLast=10401040
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SYMPK Gene

Domains & Families for SYMPK Gene

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

No data available for Gene Families for SYMPK Gene

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.

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

Gene Ontology (GO) - Cellular Components for SYMPK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA,TAS --
GO:0005737 cytoplasm IEA,IDA 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(2.7)
  • Blood(2.5)
  • Skin(2)
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 34 35
  • 99.58 (n)
dog
(Canis familiaris)
Mammalia SYMPK 34 35
  • 91.17 (n)
cow
(Bos Taurus)
Mammalia SYMPK 34 35
  • 90.67 (n)
mouse
(Mus musculus)
Mammalia Sympk 34 16 35
  • 87.99 (n)
oppossum
(Monodelphis domestica)
Mammalia SYMPK 35
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sympk 34
  • 86.93 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SYMPK 35
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYMPK 35
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sympk 34
  • 67.94 (n)
MGC75595 34
African clawed frog
(Xenopus laevis)
Amphibia MGC53503 34
zebrafish
(Danio rerio)
Actinopterygii si:dkeyp-117b8.1 34
  • 71.93 (n)
SYMPK 35
  • 68 (a)
OneToOne
Dr.4673 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.988 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002618 34
  • 53.05 (n)
fruit fly
(Drosophila melanogaster)
Insecta Sym 34 35
  • 47.39 (n)
worm
(Caenorhabditis elegans)
Secernentea symk-1 34 35
  • 41.53 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6518 35
  • 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 Sequence Context AA Info Type
rs1000077841 -- 45,843,031(+) CCGAG(C/T)GGGCA intron-variant
rs1000110757 -- 45,844,626(+) GCCGA(A/G)ATCGC intron-variant
rs1000146796 -- 45,821,610(+) GGCTG(C/G)AACAG intron-variant
rs1000159962 -- 45,858,512(+) CTGAC(C/G)ACTAT intron-variant
rs1000183332 -- 45,823,096(+) AAAGC(A/G)AGTCT 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)

Relevant External Links for SYMPK Gene

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

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

Disorders for SYMPK Gene

MalaCards: The human disease database

(1) MalaCards diseases for SYMPK Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
vein disease
  • disorder of vein
- elite association - COSMIC cancer census association via MalaCards
Search SYMPK in MalaCards View complete list of genes associated with diseases

Relevant External Links for SYMPK

Genetic Association Database (GAD)
SYMPK
Human Genome Epidemiology (HuGE) Navigator
SYMPK
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SYMPK
genes like me logo Genes that share disorders with SYMPK: view

No data available for 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 N.G. … Steitz J.A. (Genes Dev. 2005) 3 4 22 64
  2. HSF1 modulation of Hsp70 mRNA polyadenylation via interaction with symplekin. (PMID: 14707147) Xing H. … Sarge K.D. (J. Biol. Chem. 2004) 3 4 22 64
  3. Complex protein interactions within the human polyadenylation machinery identify a novel component. (PMID: 10669729) Takagaki Y. … Manley J.L. (Mol. Cell. Biol. 2000) 3 4 22 64
  4. Chromosomal localization to 19q13.3, partial genomic structure and 5' cDNA sequence of the human symplekin gene. (PMID: 9330635) Ueki K. … Louis D.N. (Somat. Cell Mol. Genet. 1997) 2 3 4 64
  5. Symplekin, a novel type of tight junction plaque protein. (PMID: 8769423) Keon B.H. … Franke W.W. (J. Cell Biol. 1996) 3 4 22 64

Products for SYMPK Gene

Sources for SYMPK Gene

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