CSDE1 (cold shock domain containing E1) - Rat Genome Database

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Gene: CSDE1 (cold shock domain containing E1) Sus scrofa
Analyze
Symbol: CSDE1
Name: cold shock domain containing E1
RGD ID: 14171185
Description: ENCODES a protein that exhibits nucleic acid binding (inferred); RISC complex binding (inferred); RNA stem-loop binding (inferred); INVOLVED IN CRD-mediated mRNA stabilization (inferred); IRES-dependent viral translational initiation (inferred); negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (inferred); ASSOCIATED WITH genetic disease (ortholog); hereditary spastic paraplegia 47 (ortholog); RASopathy (ortholog); FOUND IN mCRD-mediated mRNA stability complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: cold shock domain containing E1, RNA-binding; cold shock domain-containing protein E1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4105,804,587 - 105,845,733 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14105,804,512 - 105,845,735 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24115,990,371 - 116,034,488 (+)NCBISscrofa10.2Sscrofa10.2susScr3
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

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
CSDE1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4105,804,587 - 105,845,733 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14105,804,512 - 105,845,735 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24115,990,371 - 116,034,488 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CSDE1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381114,716,916 - 114,757,984 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1114,716,913 - 114,758,676 (-)EnsemblGRCh38hg38GRCh38
GRCh371115,259,537 - 115,300,605 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361115,061,060 - 115,102,147 (-)NCBINCBI36Build 36hg18NCBI36
Celera1113,488,779 - 113,529,908 (-)NCBICelera
Cytogenetic Map1p13.2NCBI
HuRef1113,117,993 - 113,159,121 (-)NCBIHuRef
CHM1_11115,374,336 - 115,415,479 (-)NCBICHM1_1
T2T-CHM13v2.01114,728,361 - 114,769,423 (-)NCBIT2T-CHM13v2.0
Csde1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393102,927,347 - 102,965,502 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3102,927,742 - 102,965,502 (+)EnsemblGRCm39 Ensembl
GRCm383103,020,431 - 103,058,186 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3103,020,426 - 103,058,186 (+)EnsemblGRCm38mm10GRCm38
MGSCv373102,824,469 - 102,862,112 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363103,149,692 - 103,187,240 (+)NCBIMGSCv36mm8
Celera3105,225,421 - 105,263,064 (+)NCBICelera
Cytogenetic Map3F2.2NCBI
cM Map345.25NCBI
Csde1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82193,234,546 - 193,271,301 (+)NCBIGRCr8
mRatBN7.22190,546,015 - 190,582,787 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2190,554,980 - 190,582,784 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2198,152,478 - 198,180,272 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02196,024,877 - 196,052,699 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02190,842,171 - 190,869,965 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02205,525,194 - 205,552,987 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2205,525,204 - 205,552,991 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02224,955,782 - 224,983,574 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.12198,226,179 - 198,255,228 (+)NCBI
Celera2183,028,421 - 183,056,128 (+)NCBICelera
Cytogenetic Map2q34NCBI
Csde1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543518,008,352 - 18,050,329 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543518,009,228 - 18,050,329 (-)NCBIChiLan1.0ChiLan1.0
CSDE1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21107,379,136 - 107,420,513 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11106,973,319 - 107,014,750 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0187,796,518 - 87,837,602 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11122,849,898 - 122,890,959 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1122,849,903 - 122,890,959 (+)Ensemblpanpan1.1panPan2
CSDE1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11752,418,978 - 52,458,427 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1752,420,048 - 52,458,329 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1752,069,582 - 52,109,078 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01753,296,332 - 53,335,791 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1753,296,335 - 53,335,733 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11752,330,468 - 52,369,923 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01752,372,669 - 52,412,187 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01752,945,996 - 52,985,466 (-)NCBIUU_Cfam_GSD_1.0
Csde1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505814,366,354 - 14,403,092 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493662785,894 - 122,592 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSDE1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12018,913,195 - 18,953,727 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2018,913,230 - 18,953,755 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603821,667,257 - 21,707,843 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Csde1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477210,369,447 - 10,406,718 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in CSDE1
915 total Variants

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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 10 4 3 5 2 23 2 3 3
Low
Below cutoff

Sequence


RefSeq Acc Id: ENSSSCT00000044302   ⟹   ENSSSCP00000057604
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl4105,804,604 - 105,845,733 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000048448   ⟹   ENSSSCP00000053136
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl4105,820,965 - 105,845,350 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000064093   ⟹   ENSSSCP00000050736
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl4105,804,587 - 105,845,724 (+)Ensembl
RefSeq Acc Id: XM_003481484   ⟹   XP_003481532
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.14105,804,512 - 105,845,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_005655415   ⟹   XP_005655472
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.14105,804,512 - 105,845,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_005655416   ⟹   XP_005655473
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.14105,804,512 - 105,845,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_005655417   ⟹   XP_005655474
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.14105,804,512 - 105,845,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021090004   ⟹   XP_020945663
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.14105,805,870 - 105,845,735 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021090005   ⟹   XP_020945664
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.14105,805,107 - 105,845,735 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_003481532 (Get FASTA)   NCBI Sequence Viewer  
  XP_005655472 (Get FASTA)   NCBI Sequence Viewer  
  XP_005655473 (Get FASTA)   NCBI Sequence Viewer  
  XP_005655474 (Get FASTA)   NCBI Sequence Viewer  
  XP_020945663 (Get FASTA)   NCBI Sequence Viewer  
  XP_020945664 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSSCP00000050736
  ENSSSCP00000050736.1
  ENSSSCP00000053136
  ENSSSCP00000053136.2
  ENSSSCP00000057604
  ENSSSCP00000057604.3
  ENSSSCP00005010205.1
  ENSSSCP00005010387.1
  ENSSSCP00005010407.1
  ENSSSCP00005010471.1
  ENSSSCP00015035475.1
  ENSSSCP00015035539.1
  ENSSSCP00015035748.1
  ENSSSCP00015035871.1
  ENSSSCP00025008834.1
  ENSSSCP00025008883.1
  ENSSSCP00025008918.1
  ENSSSCP00025008965.1
  ENSSSCP00030032419.1
  ENSSSCP00030032425.1
  ENSSSCP00030032555.1
  ENSSSCP00030032601.1
  ENSSSCP00035021605.1
  ENSSSCP00035021610.1
  ENSSSCP00035021615.1
  ENSSSCP00035021621.1
  ENSSSCP00040011982.1
  ENSSSCP00040012044.1
  ENSSSCP00040012078.1
  ENSSSCP00040012109.1
  ENSSSCP00045011293.1
  ENSSSCP00045011341.1
  ENSSSCP00045011424.1
  ENSSSCP00045011519.1
  ENSSSCP00050024116.1
  ENSSSCP00050024127.1
  ENSSSCP00050024138.1
  ENSSSCP00050024146.1
  ENSSSCP00055019631.1
  ENSSSCP00055019806.1
  ENSSSCP00055019966.1
  ENSSSCP00055020113.1
  ENSSSCP00060042472.1
  ENSSSCP00060042611.1
  ENSSSCP00060042652.1
  ENSSSCP00060042723.1
  ENSSSCP00065016999.1
  ENSSSCP00065017004.1
  ENSSSCP00065017007.1
  ENSSSCP00065017014.1
  ENSSSCP00065017021.1
  ENSSSCP00070007486.1
  ENSSSCP00070007495.1
  ENSSSCP00070007511.1
  ENSSSCP00070007516.1
RefSeq Acc Id: XP_003481532   ⟸   XM_003481484
- Peptide Label: isoform X1
- UniProtKB: A0A287B2T9 (UniProtKB/TrEMBL),   A0A4X1SYQ9 (UniProtKB/TrEMBL),   A0A8D1QD54 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005655472   ⟸   XM_005655415
- Peptide Label: isoform X2
- UniProtKB: A0A8D1U1C4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005655473   ⟸   XM_005655416
- Peptide Label: isoform X3
- UniProtKB: A0A8D1YCF7 (UniProtKB/TrEMBL),   A0A8D1H8A2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005655474   ⟸   XM_005655417
- Peptide Label: isoform X4
- UniProtKB: A0A4X1SYH9 (UniProtKB/TrEMBL),   A0A8D1QNR2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020945664   ⟸   XM_021090005
- Peptide Label: isoform X4
- UniProtKB: A0A4X1SYH9 (UniProtKB/TrEMBL),   A0A8D1QNR2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020945663   ⟸   XM_021090004
- Peptide Label: isoform X1
- UniProtKB: A0A287B2T9 (UniProtKB/TrEMBL),   A0A4X1SYQ9 (UniProtKB/TrEMBL),   A0A8D1QD54 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000050736   ⟸   ENSSSCT00000064093
RefSeq Acc Id: ENSSSCP00000053136   ⟸   ENSSSCT00000048448
RefSeq Acc Id: ENSSSCP00000057604   ⟸   ENSSSCT00000044302
Protein Domains
CSD   SUZ-C


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000006752 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00005010964 UniProtKB/TrEMBL
  ENSSSCG00015065030 UniProtKB/TrEMBL
  ENSSSCG00025015812 UniProtKB/TrEMBL
  ENSSSCG00030051025 UniProtKB/TrEMBL
  ENSSSCG00035040397 UniProtKB/TrEMBL
  ENSSSCG00040020719 UniProtKB/TrEMBL
  ENSSSCG00045009633 UniProtKB/TrEMBL
  ENSSSCG00050041707 UniProtKB/TrEMBL
  ENSSSCG00055012495 UniProtKB/TrEMBL
  ENSSSCG00060071559 UniProtKB/TrEMBL
  ENSSSCG00065029820 UniProtKB/TrEMBL
  ENSSSCG00070004780 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000044302 ENTREZGENE
  ENSSSCT00000044302.3 UniProtKB/TrEMBL
  ENSSSCT00000048448 ENTREZGENE
  ENSSSCT00000048448.3 UniProtKB/TrEMBL
  ENSSSCT00000064093 ENTREZGENE
  ENSSSCT00000064093.3 UniProtKB/TrEMBL
  ENSSSCT00005017135.1 UniProtKB/TrEMBL
  ENSSSCT00005017387.1 UniProtKB/TrEMBL
  ENSSSCT00005017422.1 UniProtKB/TrEMBL
  ENSSSCT00005017502.1 UniProtKB/TrEMBL
  ENSSSCT00015087079.1 UniProtKB/TrEMBL
  ENSSSCT00015087236.1 UniProtKB/TrEMBL
  ENSSSCT00015087701.1 UniProtKB/TrEMBL
  ENSSSCT00015087963.1 UniProtKB/TrEMBL
  ENSSSCT00025021488.1 UniProtKB/TrEMBL
  ENSSSCT00025021600.1 UniProtKB/TrEMBL
  ENSSSCT00025021674.1 UniProtKB/TrEMBL
  ENSSSCT00025021770.1 UniProtKB/TrEMBL
  ENSSSCT00030071091.1 UniProtKB/TrEMBL
  ENSSSCT00030071113.1 UniProtKB/TrEMBL
  ENSSSCT00030071400.1 UniProtKB/TrEMBL
  ENSSSCT00030071509.1 UniProtKB/TrEMBL
  ENSSSCT00035053694.1 UniProtKB/TrEMBL
  ENSSSCT00035053719.1 UniProtKB/TrEMBL
  ENSSSCT00035053736.1 UniProtKB/TrEMBL
  ENSSSCT00035053748.1 UniProtKB/TrEMBL
  ENSSSCT00040028507.1 UniProtKB/TrEMBL
  ENSSSCT00040028702.1 UniProtKB/TrEMBL
  ENSSSCT00040028784.1 UniProtKB/TrEMBL
  ENSSSCT00040028869.1 UniProtKB/TrEMBL
  ENSSSCT00045016345.1 UniProtKB/TrEMBL
  ENSSSCT00045016419.1 UniProtKB/TrEMBL
  ENSSSCT00045016559.1 UniProtKB/TrEMBL
  ENSSSCT00045016701.1 UniProtKB/TrEMBL
  ENSSSCT00050056618.1 UniProtKB/TrEMBL
  ENSSSCT00050056634.1 UniProtKB/TrEMBL
  ENSSSCT00050056646.1 UniProtKB/TrEMBL
  ENSSSCT00050056661.1 UniProtKB/TrEMBL
  ENSSSCT00055024731.1 UniProtKB/TrEMBL
  ENSSSCT00055024949.1 UniProtKB/TrEMBL
  ENSSSCT00055025129.1 UniProtKB/TrEMBL
  ENSSSCT00055025317.1 UniProtKB/TrEMBL
  ENSSSCT00060097979.1 UniProtKB/TrEMBL
  ENSSSCT00060098299.1 UniProtKB/TrEMBL
  ENSSSCT00060098368.1 UniProtKB/TrEMBL
  ENSSSCT00060098500.1 UniProtKB/TrEMBL
  ENSSSCT00065040225.1 UniProtKB/TrEMBL
  ENSSSCT00065040234.1 UniProtKB/TrEMBL
  ENSSSCT00065040241.1 UniProtKB/TrEMBL
  ENSSSCT00065040254.1 UniProtKB/TrEMBL
  ENSSSCT00065040271.1 UniProtKB/TrEMBL
  ENSSSCT00070009123.1 UniProtKB/TrEMBL
  ENSSSCT00070009136.1 UniProtKB/TrEMBL
  ENSSSCT00070009156.1 UniProtKB/TrEMBL
  ENSSSCT00070009164.1 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.140 UniProtKB/TrEMBL
InterPro Cold-shock_CS UniProtKB/TrEMBL
  CSD UniProtKB/TrEMBL
  CSP_DNA-bd UniProtKB/TrEMBL
  NA-bd_OB-fold UniProtKB/TrEMBL
  SUZ-C UniProtKB/TrEMBL
KEGG Report ssc:100739316 UniProtKB/TrEMBL
NCBI Gene CSDE1 ENTREZGENE
PANTHER COLD SHOCK DOMAIN-CONTAINING PROTEIN E1 UniProtKB/TrEMBL
  UNR PROTEIN N-RAS UPSTREAM GENE PROTEIN UniProtKB/TrEMBL
Pfam CSD UniProtKB/TrEMBL
  SUZ-C UniProtKB/TrEMBL
PROSITE COLD_SHOCK UniProtKB/TrEMBL
  CSD_2 UniProtKB/TrEMBL
  SUZ_C UniProtKB/TrEMBL
SMART CSP UniProtKB/TrEMBL
Superfamily-SCOP SSF50249 UniProtKB/TrEMBL
UniProt A0A287B2T9 ENTREZGENE, UniProtKB/TrEMBL
  A0A287B9X6_PIG UniProtKB/TrEMBL
  A0A287BM79_PIG UniProtKB/TrEMBL
  A0A4X1SYB4_PIG UniProtKB/TrEMBL
  A0A4X1SYH9 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1SYQ9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0IKZ0_PIG UniProtKB/TrEMBL
  A0A8D0LHH7_PIG UniProtKB/TrEMBL
  A0A8D0PLX0_PIG UniProtKB/TrEMBL
  A0A8D0U9K3_PIG UniProtKB/TrEMBL
  A0A8D1H8A2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1MGY3_PIG UniProtKB/TrEMBL
  A0A8D1QD54 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1QNR2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1U1C4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1WSG4_PIG UniProtKB/TrEMBL
  A0A8D1YCF7 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:87029 ENTREZGENE