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Aliases for CSDC2 Gene

Aliases for CSDC2 Gene

  • Cold Shock Domain Containing C2 2 3 5
  • Cold Shock Domain Containing C2, RNA Binding 2 3
  • PIPPIN 3 4
  • Cold Shock Domain-Containing Protein C2 3
  • RNA-Binding Protein Pippin 3
  • RNA-Binding Protein PIPPin 4
  • DJ347H13.2 3

External Ids for CSDC2 Gene

Previous GeneCards Identifiers for CSDC2 Gene

  • GC22P040282
  • GC22P041956
  • GC22P024922

Summaries for CSDC2 Gene

GeneCards Summary for CSDC2 Gene

CSDC2 (Cold Shock Domain Containing C2) is a Protein Coding gene. GO annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is CARHSP1.

UniProtKB/Swiss-Prot for CSDC2 Gene

  • RNA-binding factor which binds specifically to the very 3-UTR ends of both histone H1 and H3.3 mRNAs, encompassing the polyadenylation signal. Might play a central role in the negative regulation of histone variant synthesis in the developing brain (By similarity).

Gene Wiki entry for CSDC2 Gene

Additional gene information for CSDC2 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CSDC2 Gene

Genomics for CSDC2 Gene

Regulatory Elements for CSDC2 Gene

Enhancers for CSDC2 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
GH22H041559 1.5 Ensembl ENCODE dbSUPER 15.6 +2.3 2320 6 HDGF PKNOX1 TCF12 ZNF121 GLIS2 FOS REST ZNF662 ZNF592 MEF2D MEI1 POLR3H CSDC2 XRCC6 DESI1 PHF5A SLC25A17 EP300 RANGAP1 CENPM
GH22H041417 1.3 Ensembl ENCODE dbSUPER 15.6 -142.6 -142638 1 FOXA2 TAF1 MAX ZIC2 RAD21 YY1 HIC1 ZNF121 GATA3 GLIS2 CSDC2 MEI1 GC22P041413 ENSG00000273424
GH22H041831 1.4 ENCODE dbSUPER 13.7 +272.4 272439 4 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 CYP2D8P MEI1 L3MBTL2 NDUFA6-AS1 CSDC2 CYP2D6 DESI1 RNU6ATAC22P ZC3H7B OGFRP1
GH22H041393 0.7 ENCODE dbSUPER 24 -166.3 -166330 1 MAX HNF4A CSDC2 TEF POLR3H ACO2 PHF5A PIR38134 LOC105373042
GH22H041467 1.6 Ensembl ENCODE dbSUPER 10.4 -89.9 -89934 7 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF143 POLR3H MEI1 PHF5A TOB2 EP300 NAGA CSDC2 FAM109B ENSG00000232754 SMDT1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CSDC2 on UCSC Golden Path with GeneCards custom track

Genomic Location for CSDC2 Gene

Chromosome:
22
Start:
41,560,763 bp from pter
End:
41,577,741 bp from pter
Size:
16,979 bases
Orientation:
Plus strand

Genomic View for CSDC2 Gene

Genes around CSDC2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CSDC2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CSDC2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CSDC2 Gene

Proteins for CSDC2 Gene

  • Protein details for CSDC2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y534-CSDC2_HUMAN
    Recommended name:
    Cold shock domain-containing protein C2
    Protein Accession:
    Q9Y534
    Secondary Accessions:
    • Q8ND37

    Protein attributes for CSDC2 Gene

    Size:
    153 amino acids
    Molecular mass:
    16786 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CSDC2 Gene

Post-translational modifications for CSDC2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CSDC2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CSDC2 Gene

Domains & Families for CSDC2 Gene

Gene Families for CSDC2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for CSDC2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CSDC2: view

No data available for UniProtKB/Swiss-Prot for CSDC2 Gene

Function for CSDC2 Gene

Molecular function for CSDC2 Gene

UniProtKB/Swiss-Prot Function:
RNA-binding factor which binds specifically to the very 3-UTR ends of both histone H1 and H3.3 mRNAs, encompassing the polyadenylation signal. Might play a central role in the negative regulation of histone variant synthesis in the developing brain (By similarity).

Phenotypes From GWAS Catalog for CSDC2 Gene

Gene Ontology (GO) - Molecular Function for CSDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding NAS 12801884
GO:0003730 mRNA 3-UTR binding IBA --
GO:0005515 protein binding IPI 25416956
GO:0008134 transcription factor binding IEA --
genes like me logo Genes that share ontologies with CSDC2: view
genes like me logo Genes that share phenotypes with CSDC2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CSDC2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CSDC2 Gene

Localization for CSDC2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CSDC2 Gene

Nucleus. Cytoplasm. Note=PIPPin-RNA complexes are located to the nucleus. {ECO:0000250}.

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 CSDC2 gene
Compartment Confidence
nucleus 4
cytosol 3
extracellular 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for CSDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IBA --
genes like me logo Genes that share ontologies with CSDC2: view

Pathways & Interactions for CSDC2 Gene

SuperPathways for CSDC2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CSDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006397 mRNA processing IEA --
GO:0043488 regulation of mRNA stability IBA --
genes like me logo Genes that share ontologies with CSDC2: view

No data available for Pathways by source and SIGNOR curated interactions for CSDC2 Gene

Drugs & Compounds for CSDC2 Gene

(1) Drugs for CSDC2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with CSDC2: view

Transcripts for CSDC2 Gene

mRNA/cDNA for CSDC2 Gene

Unigene Clusters for CSDC2 Gene

Cold shock domain containing C2, RNA binding:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CSDC2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for CSDC2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5
SP1: -
SP2:

Relevant External Links for CSDC2 Gene

GeneLoc Exon Structure for
CSDC2
ECgene alternative splicing isoforms for
CSDC2

Expression for CSDC2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CSDC2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CSDC2 Gene

This gene is overexpressed in Heart - Left Ventricle (x8.9) and Heart - Atrial Appendage (x6.1).

Protein differential expression in normal tissues from HIPED for CSDC2 Gene

This gene is overexpressed in Testis (17.9), Ovary (14.1), Heart (14.0), and Breast (12.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CSDC2 Gene



NURSA nuclear receptor signaling pathways regulating expression of CSDC2 Gene:

CSDC2

SOURCE GeneReport for Unigene cluster for CSDC2 Gene:

Hs.310893

Evidence on tissue expression from TISSUES for CSDC2 Gene

  • Nervous system(4.8)
  • Intestine(4.2)
genes like me logo Genes that share expression patterns with CSDC2: view

Primer Products

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CSDC2 Gene

Orthologs for CSDC2 Gene

This gene was present in the common ancestor of animals.

Orthologs for CSDC2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CSDC2 34
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CSDC2 33 34
  • 91.07 (n)
oppossum
(Monodelphis domestica)
Mammalia CSDC2 34
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CSDC2 33 34
  • 89.76 (n)
mouse
(Mus musculus)
Mammalia Csdc2 33 16 34
  • 88.67 (n)
rat
(Rattus norvegicus)
Mammalia Csdc2 33
  • 87.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CSDC2 34
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves CSDC2 33 34
  • 81.05 (n)
lizard
(Anolis carolinensis)
Reptilia CSDC2 34
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia csdc2 33
  • 73.29 (n)
zebrafish
(Danio rerio)
Actinopterygii csdc2a 33 34
  • 64.29 (n)
csdc2b 34
  • 59 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG9705 34
  • 46 (a)
OneToMany
Species where no ortholog for CSDC2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for CSDC2 Gene

ENSEMBL:
Gene Tree for CSDC2 (if available)
TreeFam:
Gene Tree for CSDC2 (if available)

Paralogs for CSDC2 Gene

Paralogs for CSDC2 Gene

(1) SIMAP similar genes for CSDC2 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with CSDC2: view

Variants for CSDC2 Gene

Sequence variations from dbSNP and Humsavar for CSDC2 Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs1000216959 -- 41,564,099(+) AAAAA(-/AAAAG)AAGAA intron-variant
rs1000235345 -- 41,574,928(+) GGGGG(C/T)TGGGG utr-variant-3-prime
rs1000327788 -- 41,561,353(+) TTCTC(G/T)CCCCG intron-variant, upstream-variant-2KB
rs1000339302 -- 41,569,253(+) TCTTC(-/T)TTTTT intron-variant
rs1000383062 -- 41,567,786(+) CCTCT(C/T)TGAGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CSDC2 Gene

Variant ID Type Subtype PubMed ID
esv3647800 CNV gain 21293372
nsv1055166 CNV gain 25217958
nsv3639 CNV insertion 18451855
nsv516925 CNV loss 19592680
nsv524585 CNV loss 19592680
nsv834209 CNV loss 17160897

Variation tolerance for CSDC2 Gene

Residual Variation Intolerance Score: 51.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.67; 14.36% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CSDC2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CSDC2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CSDC2 Gene

Disorders for CSDC2 Gene

Relevant External Links for CSDC2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CSDC2

No disorders were found for CSDC2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CSDC2 Gene

Publications for CSDC2 Gene

  1. PIPPin, a putative RNA-binding protein specifically expressed in the rat brain. (PMID: 8573167) Castiglia D … Di Liegro I (Biochemical and biophysical research communications 1996) 2 3 22 60
  2. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins JE … Dunham I (Genome biology 2004) 3 4 60
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  4. RNA-binding ability of PIPPin requires the entire protein. (PMID: 12767259) Raimondi L … Di Liegro I (Journal of cellular and molecular medicine 2003) 2 3 60
  5. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I … O'Brien KP (Nature 1999) 3 4 60

Products for CSDC2 Gene

Sources for CSDC2 Gene

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