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
  • Cold Shock Domain-Containing Protein C2 3 4
  • 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. Diseases associated with CSDC2 include Morgagni Cataract and Pick Disease Of Brain. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is CARHSP1.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for CSDC2 Gene

Genomics for CSDC2 Gene

GeneHancer (GH) Regulatory Elements for CSDC2 Gene

Promoters and enhancers for CSDC2 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
GH22J041559 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 515.5 +2.1 2072 6.9 EP300 NRF1 JUND TEAD4 FOS ZIC2 REST TRIM28 TOE1 MYC CSDC2 POLR3H MEI1 DESI1 XRCC6 TEF PHF5A SLC25A17 EP300 RANGAP1
GH22J041467 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 14.8 -85.5 -85529 16.3 EP300 FOXK2 ZBTB40 ZNF217 SIN3A NRF1 MYC POLR2G SP1 NCOR1 PHF5A ACO2 EP300 POLR3H XRCC6 ENSG00000232754 ZC3H7B L3MBTL2 ENSG00000235513 SNU13
GH22J041831 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 13.7 +272.2 272192 4.2 EP300 FOXK2 HNRNPK ZBTB40 ZNF217 SIN3A NRF1 TCF12 POLR2G SP1 SREBF2 SREBF2-AS1 piR-38064 piR-34985 piR-32612 piR-38684 piR-36461 piR-61267 CYP2D8P MEI1
GH22J041799 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 8.7 +239.8 239817 3.4 ZBTB40 SIN3A NRF1 POLR2G SP1 ZNF639 ZIC2 POLR2A ZBTB11 GABPA CCDC134 lnc-SNU13-3 MEI1 DESI1 L3MBTL2 RRP7BP ZC3H7B CSDC2 NDUFA6 piR-61427
GH22J041393 Enhancer 0.8 Ensembl ENCODE dbSUPER 24 -167.0 -166965 2.1 RXRA HNF4A MAX SP1 CSDC2 TEF POLR3H PHF5A ACO2 SMDT1 piR-45135 LOC105373042
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CSDC2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CSDC2

Top Transcription factor binding sites by QIAGEN in the CSDC2 gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • Chx10
  • CP1A
  • NF-1
  • NF-Y
  • NF-YA
  • NF-YB
  • RP58

Genomic Locations for CSDC2 Gene

Genomic Locations for CSDC2 Gene
chr22:41,561,010-41,577,741
(GRCh38/hg38)
Size:
16,732 bases
Orientation:
Plus strand
chr22:41,956,767-41,973,745
(GRCh37/hg19)
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

Protein Domains for CSDC2 Gene

Blocks:
  • Cold-shock DNA-binding domain
  • Cold shock protein
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CSDC2 Gene

GenScript: Design optimal peptide antigens:
  • RNA-binding protein PIPPin (CSDC2_HUMAN)
genes like me logo Genes that share domains with CSDC2: view

No data available for Graphical View of Domain Structure and 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:0003723 RNA binding NAS 12801884
GO:0003730 mRNA 3'-UTR binding IBA 21873635
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

Clone Products

  • Addgene plasmids for CSDC2

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
plasma membrane 1
extracellular 1
cytoskeleton 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 21873635
genes like me logo Genes that share ontologies with CSDC2: view

Pathways & Interactions for CSDC2 Gene

PathCards logo

SuperPathways for CSDC2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CSDC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006397 mRNA processing IEA --
GO:0043488 regulation of mRNA stability IBA 21873635
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

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for CSDC2

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

Expression for CSDC2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for CSDC2 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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

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 31
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CSDC2 31 30
  • 91.07 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CSDC2 31
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CSDC2 31 30
  • 89.76 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Csdc2 17 31 30
  • 88.67 (n)
rat
(Rattus norvegicus)
Mammalia Csdc2 30
  • 87.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CSDC2 31
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves CSDC2 31 30
  • 81.05 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CSDC2 31
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia csdc2 30
  • 73.29 (n)
zebrafish
(Danio rerio)
Actinopterygii csdc2a 31 30
  • 64.29 (n)
OneToMany
csdc2b 31
  • 59 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG9705 31
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for CSDC2: view image

Paralogs for CSDC2 Gene

Paralogs for CSDC2 Gene

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

  • CSDC2_HUMAN
  • H7C4E7_HUMAN
genes like me logo Genes that share paralogs with CSDC2: view

Variants for CSDC2 Gene

Additional dbSNP identifiers (rs#s) for CSDC2 Gene

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)

Additional Variant Information for CSDC2 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CSDC2 Gene

Disorders for CSDC2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CSDC2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
morgagni cataract
  • hypermature cataract
pick disease of brain
  • lobar atrophy of brain
- elite association - COSMIC cancer census association via MalaCards
Search CSDC2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CSDC2

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

No data available for 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 23 54
  2. 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 54
  3. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins JE … Dunham I (Genome biology 2004) 3 4 54
  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 54
  5. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I … O'Brien KP (Nature 1999) 3 4 54

Products for CSDC2 Gene

Sources for CSDC2 Gene