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Aliases for CSDC2 Gene

Aliases for CSDC2 Gene

  • Cold Shock Domain Containing C2 2 3
  • Cold Shock Domain Containing C2, RNA Binding 2 3 5
  • PIPPIN 3 4
  • 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

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

Genomics for CSDC2 Gene

Regulatory Elements for CSDC2 Gene

Promoters for CSDC2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs 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

Proteomics data for CSDC2 Gene at MOPED

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

Suggested Antigen Peptide Sequences for CSDC2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y534

UniProtKB/Swiss-Prot:

CSDC2_HUMAN :
  • Contains 1 CSD (cold-shock) domain.
Domain:
  • Contains 1 CSD (cold-shock) domain.
genes like me logo Genes that share domains with CSDC2: view

No data available for Gene Families 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).

Gene Ontology (GO) - Molecular Function for CSDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
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

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
Jensen Localization Image for CSDC2 Gene COMPARTMENTS Subcellular localization image for CSDC2 gene
Compartment Confidence
nucleus 4
cytosol 3
extracellular 1

No data available for Gene Ontology (GO) - Cellular Components for CSDC2 Gene

Pathways & Interactions for CSDC2 Gene

SuperPathways for CSDC2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CSDC2 Gene

None

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:

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 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, MOPED, and MaxQB for CSDC2 Gene



SOURCE GeneReport for Unigene cluster for CSDC2 Gene Hs.310893

genes like me logo Genes that share expression patterns with CSDC2: view

Primer Products

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners 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 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CSDC2 36
  • 95 (a)
OneToOne
CSDC2 35
  • 91.07 (n)
  • 94.77 (a)
dog
(Canis familiaris)
Mammalia CSDC2 35
  • 89.76 (n)
  • 93.46 (a)
CSDC2 36
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Csdc2 16
Csdc2 35
  • 88.67 (n)
  • 96.73 (a)
Csdc2 36
  • 96 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CSDC2 36
  • 91 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CSDC2 36
  • 84 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Csdc2 35
  • 87.8 (n)
  • 98.04 (a)
chicken
(Gallus gallus)
Aves CSDC2 35
  • 81.05 (n)
  • 88.24 (a)
CSDC2 36
  • 83 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CSDC2 36
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia csdc2 35
  • 73.29 (n)
  • 80.13 (a)
zebrafish
(Danio rerio)
Actinopterygii csdc2a 36
  • 65 (a)
OneToMany
csdc2b 36
  • 59 (a)
OneToMany
csdc2a 35
  • 64.29 (n)
  • 67.14 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG9705 36
  • 46 (a)
OneToMany
Species with no ortholog for CSDC2:
  • 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
rs172149 -- 41,566,541(+) cagga(A/G)aatca intron-variant
rs1006407 -- 41,576,028(+) CTGTC(C/T)GCCTC utr-variant-3-prime
rs2064164 -- 41,570,669(+) ATACA(A/C)AAATT intron-variant
rs3885552 -- 41,570,102(-) GCAAG(C/G)TTCAA intron-variant
rs4822039 -- 41,565,130(+) cactg(A/G)actcc intron-variant

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

Variant ID Type Subtype PubMed ID
nsv524585 CNV Loss 19592680
nsv516925 CNV Loss 19592680
nsv834209 CNV Loss 17160897
nsv3639 CNV Insertion 18451855

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

HapMap Linkage Disequilibrium report
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. (Biochem. Biophys. Res. Commun. 1996) 2 3 23 67
  2. RNA-binding ability of PIPPin requires the entire protein. (PMID: 12767259) Raimondi L. … Di Liegro I. (J. Cell. Mol. Med. 2003) 2 3
  3. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3
  4. Doc2b is a high-affinity Ca2+ sensor for spontaneous neurotransmitter release. (PMID: 20150444) Groffen A.J. … Verhage M. (Science 2010) 23
  5. Organization and synergistic binding of copine I and annexin A1 on supported lipid bilayers observed by atomic force microscopy. (PMID: 19539605) Creutz C.E. … Edwardson J.M. (Biochim. Biophys. Acta 2009) 23

Products for CSDC2 Gene

Sources for CSDC2 Gene

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