CSDC2 (cold shock domain containing C2) - Rat Genome Database

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Gene: CSDC2 (cold shock domain containing C2) Homo sapiens
Analyze
Symbol: CSDC2
Name: cold shock domain containing C2
RGD ID: 1603657
HGNC Page HGNC
Description: Predicted to enable mRNA 3'-UTR binding activity. Predicted to be involved in regulation of mRNA stability. Predicted to be located in nucleus. Predicted to be active in cytoplasm; INTERACTS WITH acrylamide; aflatoxin B1; beauvericin.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: cold shock domain containing C2, RNA binding; cold shock domain-containing protein C2; dJ347H13.2; PIPPIN; RNA-binding protein pippin
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2241,561,010 - 41,577,741 (+)EnsemblGRCh38hg38GRCh38
GRCh382241,561,010 - 41,576,666 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372241,957,014 - 41,972,670 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362240,286,960 - 40,302,616 (+)NCBINCBI36hg18NCBI36
Celera2225,763,426 - 25,779,097 (+)NCBI
Cytogenetic Map22q13.2NCBI
HuRef2224,922,829 - 24,938,486 (+)NCBIHuRef
CHM1_12241,916,938 - 41,932,809 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)
nucleus  (IEA,ISO)

Molecular Function

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8573167   PMID:8619474   PMID:9110174   PMID:10446180   PMID:10591208   PMID:10923677   PMID:12477932   PMID:12767259   PMID:12801884   PMID:15461802   PMID:15489334   PMID:16344560  
PMID:17474147   PMID:18029348   PMID:21873635   PMID:25416956   PMID:30078185   PMID:31515488   PMID:32296183  


Genomics

Comparative Map Data
CSDC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2241,561,010 - 41,577,741 (+)EnsemblGRCh38hg38GRCh38
GRCh382241,561,010 - 41,576,666 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372241,957,014 - 41,972,670 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362240,286,960 - 40,302,616 (+)NCBINCBI36hg18NCBI36
Celera2225,763,426 - 25,779,097 (+)NCBI
Cytogenetic Map22q13.2NCBI
HuRef2224,922,829 - 24,938,486 (+)NCBIHuRef
CHM1_12241,916,938 - 41,932,809 (+)NCBICHM1_1
Csdc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391581,820,960 - 81,835,142 (+)NCBIGRCm39mm39
GRCm39 Ensembl1581,820,960 - 81,835,142 (+)Ensembl
GRCm381581,936,759 - 81,950,941 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1581,936,759 - 81,950,941 (+)EnsemblGRCm38mm10GRCm38
MGSCv371581,767,189 - 81,781,371 (+)NCBIGRCm37mm9NCBIm37
MGSCv361581,764,191 - 81,778,196 (+)NCBImm8
Celera1584,057,995 - 84,072,989 (+)NCBICelera
Cytogenetic Map15E1NCBI
Csdc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27113,451,998 - 113,466,464 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7113,451,998 - 113,466,463 (+)Ensembl
Rnor_6.07123,168,811 - 123,183,336 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,168,811 - 123,183,335 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07123,144,206 - 123,158,717 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47120,290,137 - 120,323,640 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17120,324,478 - 120,357,857 (+)NCBI
Celera7109,770,665 - 109,782,328 (+)NCBICelera
Cytogenetic Map7q34NCBI
Csdc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541327,079,280 - 27,090,082 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541327,079,280 - 27,090,082 (+)NCBIChiLan1.0ChiLan1.0
CSDC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12240,542,255 - 40,558,513 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2240,542,255 - 40,558,513 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02222,455,605 - 22,471,836 (+)NCBIMhudiblu_PPA_v0panPan3
CSDC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11023,706,962 - 23,717,078 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1023,709,176 - 23,711,093 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1023,639,685 - 23,651,642 (-)NCBI
ROS_Cfam_1.01024,451,816 - 24,461,938 (-)NCBI
UMICH_Zoey_3.11024,168,636 - 24,178,747 (-)NCBI
UNSW_CanFamBas_1.01024,489,855 - 24,499,957 (-)NCBI
UU_Cfam_GSD_1.01024,663,942 - 24,674,057 (-)NCBI
Csdc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049457,357,797 - 7,361,402 (-)NCBI
SpeTri2.0NW_004936492368,211 - 371,834 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSDC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl56,975,840 - 6,988,422 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.156,976,121 - 6,988,604 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.254,349,492 - 4,351,976 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CSDC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11924,102,231 - 24,117,242 (+)NCBI
ChlSab1.1 Ensembl1924,112,447 - 24,115,453 (+)Ensembl
Vero_WHO_p1.0NW_023666045101,297,051 - 101,312,660 (-)NCBI
Csdc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247527,047,262 - 7,058,818 (-)NCBI

Position Markers
STS-F10883  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372241,972,496 - 41,972,669UniSTSGRCh37
Build 362240,302,442 - 40,302,615RGDNCBI36
Celera2225,778,923 - 25,779,096RGD
Cytogenetic Map22q13.2UniSTS
HuRef2224,938,312 - 24,938,485UniSTS
GeneMap99-GB4 RH Map22127.53UniSTS
RH47292  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372241,972,993 - 41,973,120UniSTSGRCh37
Build 362240,302,939 - 40,303,066RGDNCBI36
Celera2225,779,420 - 25,779,547RGD
Cytogenetic Map22q13.2UniSTS
HuRef2224,938,809 - 24,938,936UniSTS
GeneMap99-GB4 RH Map22126.64UniSTS
NCBI RH Map22195.1UniSTS
A005T18  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372241,972,494 - 41,972,666UniSTSGRCh37
Build 362240,302,440 - 40,302,612RGDNCBI36
Celera2225,778,921 - 25,779,093RGD
Cytogenetic Map22q13.2UniSTS
HuRef2224,938,310 - 24,938,482UniSTS
GeneMap99-GB4 RH Map22126.64UniSTS
NCBI RH Map22195.1UniSTS

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
MIR373hsa-miR-373-3pMirtarbaseexternal_infoqRT-PCR//ChIPFunctional MTI (Weak)18227514

Predicted Target Of
Summary Value
Count of predictions:1467
Count of miRNA genes:735
Interacting mature miRNAs:855
Transcripts:ENST00000306149, ENST00000460790
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 973 2185 611 8 25 8 1207 885 2983 219 1151 562 392 997
Low 1321 91 800 338 475 191 2862 1235 700 90 220 846 152 802 1718 1
Below cutoff 78 689 241 222 961 210 247 66 28 81 61 120 17 10 73 4

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000306149   ⟹   ENSP00000302485
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2241,561,010 - 41,576,666 (+)Ensembl
RefSeq Acc Id: ENST00000460790   ⟹   ENSP00000417127
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2241,572,017 - 41,577,741 (+)Ensembl
RefSeq Acc Id: NM_014460   ⟹   NP_055275
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382241,561,010 - 41,576,666 (+)NCBI
GRCh372241,957,014 - 41,972,670 (+)RGD
Build 362240,286,960 - 40,302,616 (+)NCBI Archive
Celera2225,763,426 - 25,779,097 (+)RGD
HuRef2224,922,829 - 24,938,486 (+)RGD
CHM1_12241,916,938 - 41,932,809 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_055275   ⟸   NM_014460
- UniProtKB: Q9Y534 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000302485   ⟸   ENST00000306149
RefSeq Acc Id: ENSP00000417127   ⟸   ENST00000460790
Protein Domains
CSD

Promoters
RGD ID:13604264
Promoter ID:EPDNEW_H28316
Type:initiation region
Name:CSDC2_1
Description:cold shock domain containing C2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H28317  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382241,560,758 - 41,560,818EPDNEW
RGD ID:13604268
Promoter ID:EPDNEW_H28317
Type:initiation region
Name:CSDC2_2
Description:cold shock domain containing C2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H28316  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382241,561,121 - 41,561,181EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 22q12.3-13.33(chr22:37061769-50738932)x3 copy number gain See cases [RCV000051684] Chr22:37061769..50738932 [GRCh38]
Chr22:37457809..51177360 [GRCh37]
Chr22:35787755..49524226 [NCBI36]
Chr22:22q12.3-13.33
pathogenic
GRCh38/hg38 22q12.3-13.33(chr22:33768441-50739977)x3 copy number gain See cases [RCV000051682] Chr22:33768441..50739977 [GRCh38]
Chr22:34164428..51178405 [GRCh37]
Chr22:32494428..49525271 [NCBI36]
Chr22:22q12.3-13.33
pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916608-50739836)x3 copy number gain See cases [RCV000133646] Chr22:16916608..50739836 [GRCh38]
Chr22:17397498..51178264 [GRCh37]
Chr22:15777498..49525130 [NCBI36]
Chr22:22q11.1-13.33
pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916743-50739785)x3 copy number gain See cases [RCV000134730] Chr22:16916743..50739785 [GRCh38]
Chr22:17397633..51178213 [GRCh37]
Chr22:15777633..49525079 [NCBI36]
Chr22:22q11.1-13.33
pathogenic
GRCh38/hg38 22q13.1-13.33(chr22:40202014-50735806)x3 copy number gain See cases [RCV000134513] Chr22:40202014..50735806 [GRCh38]
Chr22:40598018..51174234 [GRCh37]
Chr22:38927964..49521100 [NCBI36]
Chr22:22q13.1-13.33
pathogenic
GRCh38/hg38 22q13.2(chr22:41277822-42414957)x3 copy number gain See cases [RCV000136785] Chr22:41277822..42414957 [GRCh38]
Chr22:41673826..42810963 [GRCh37]
Chr22:40003772..41140907 [NCBI36]
Chr22:22q13.2
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51237518)x3 copy number gain See cases [RCV000240091] Chr22:16054691..51237518 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q12.3-13.33(chr22:35728929-51220961)x3 copy number gain See cases [RCV000240469] Chr22:35728929..51220961 [GRCh37]
Chr22:22q12.3-13.33
pathogenic
GRCh37/hg19 22q13.1-13.33(chr22:40425714-51220961)x3 copy number gain See cases [RCV000240459] Chr22:40425714..51220961 [GRCh37]
Chr22:22q13.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51220902)x3 copy number gain See cases [RCV000446956] Chr22:16054691..51220902 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054691-51237463)x3 copy number gain See cases [RCV000448847] Chr22:16054691..51237463 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q13.2(chr22:41835094-42756616)x3 copy number gain See cases [RCV000511241] Chr22:41835094..42756616 [GRCh37]
Chr22:22q13.2
uncertain significance
GRCh37/hg19 22q11.1-13.33(chr22:16888900-51197838) copy number gain See cases [RCV000510873] Chr22:16888900..51197838 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16888900-51197838)x3 copy number gain See cases [RCV000512333] Chr22:16888900..51197838 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
NC_000022.11:g.(?_41301335)_(42070317_?)del deletion Common variable immunodeficiency 4 [RCV000648330] Chr22:41301335..42070317 [GRCh38]
Chr22:41697339..42466321 [GRCh37]
Chr22:22q13.2
uncertain significance
GRCh37/hg19 22q13.2(chr22:41849322-42756616)x3 copy number gain not provided [RCV000684486] Chr22:41849322..42756616 [GRCh37]
Chr22:22q13.2
likely pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16054667-51243435)x3 copy number gain not provided [RCV000741689] Chr22:16054667..51243435 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16114244-51195728)x3 copy number gain not provided [RCV000741691] Chr22:16114244..51195728 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q11.1-13.33(chr22:16114244-51211392)x3 copy number gain not provided [RCV000741692] Chr22:16114244..51211392 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q13.2(chr22:41871935-42026428)x1 copy number loss not provided [RCV001007503] Chr22:41871935..42026428 [GRCh37]
Chr22:22q13.2
uncertain significance
GRCh37/hg19 22q11.1-13.33(chr22:16888899-51197838)x3 copy number gain not provided [RCV000846344] Chr22:16888899..51197838 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
GRCh37/hg19 22q13.1-13.33(chr22:40502364-51197838)x3 copy number gain not provided [RCV001007502] Chr22:40502364..51197838 [GRCh37]
Chr22:22q13.1-13.33
pathogenic
GRCh37/hg19 22q12.2-13.33(chr22:30654764-51197838)x3 copy number gain not provided [RCV001007181] Chr22:30654764..51197838 [GRCh37]
Chr22:22q12.2-13.33
pathogenic
GRCh37/hg19 22q13.2(chr22:41853620-42385978)x1 copy number loss not provided [RCV001258783] Chr22:41853620..42385978 [GRCh37]
Chr22:22q13.2
uncertain significance
GRCh37/hg19 22q11.1-13.33(chr22:16197005-51224252)x3 copy number gain See cases [RCV001263056] Chr22:16197005..51224252 [GRCh37]
Chr22:22q11.1-13.33
pathogenic
NC_000022.10:g.(?_41697339)_(42466321_?)del deletion Common variable immunodeficiency 4 [RCV001305750] Chr22:41697339..42466321 [GRCh37]
Chr22:22q13.2
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:30359 AgrOrtholog
COSMIC CSDC2 COSMIC
Ensembl Genes ENSG00000172346 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000302485 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000417127 UniProtKB/TrEMBL
Ensembl Transcript ENST00000306149 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000460790 UniProtKB/TrEMBL
GTEx ENSG00000172346 GTEx
HGNC ID HGNC:30359 ENTREZGENE
Human Proteome Map CSDC2 Human Proteome Map
InterPro CSD UniProtKB/Swiss-Prot
  CSD_1 UniProtKB/Swiss-Prot
  CSP_DNA-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA-bd_OB-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:27254 UniProtKB/Swiss-Prot
NCBI Gene 27254 ENTREZGENE
OMIM 617689 OMIM
Pfam CSD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA142672071 PharmGKB
PROSITE CSD_1 UniProtKB/Swiss-Prot
  CSD_2 UniProtKB/Swiss-Prot
SMART CSP UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50249 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CSDC2_HUMAN UniProtKB/Swiss-Prot
  H7C4E7_HUMAN UniProtKB/TrEMBL
  Q9Y534 ENTREZGENE
UniProt Secondary Q8ND37 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-07 CSDC2  cold shock domain containing C2    cold shock domain containing C2, RNA binding  Symbol and/or name change 5135510 APPROVED