H-InvDB x AHG DB
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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000001798 Accession number: AF077054 Created date: 26-Mar-2013 Last modified: 26-Mar-2013
Definition: Similar to Cold shock domain-containing protein E1; Protein UNR; Fragment;
 
 

Transcript original information
Accession number AF077054.1
CAGE tag ID NA
EST ID NA
Clone Number NA
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (CSDE1) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (CSDE1);
Sequence data provider Provider:CHGC
Annotation project H-Invitational FLcDNA
Length of cDNA 3581[bp] (No. of exon:19)[A:1093 T:1016 G:796 C:676]
Devision HTC
Molecular type mRNA
Library origin Cell type NA
Tissue type pituitary
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 3573(+)
Vector/adapter sequence NA
Frame shift 694-694[bp] Insertion(A);
Remaining intron NA
Splice site acceptor (NAGNAG) CAGGAG;  TAGGAG; 
Transcript quality feature Truncation; 
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0000915
Genomic location  G-integra Help Chromosome 1
Location 1p13.2
Position 115259952- 115300578
Strand -
Possible duplicated location(s) NA
Gene structure 19 exon(s)
Database links RefSeq NM_002524NM_007158NM_001007553NM_001130523
Ensembl ENST00000261443ENST00000339438ENST00000358528ENST00000369530ENST00000369535ENST00000438362ENST00000483030ENST00000483407ENST00000524652ENST00000525132ENST00000525878ENST00000525970ENST00000529046ENST00000530784ENST00000530886ENST00000533818ENST00000534389ENST00000534699
Entrez Gene Entrez Gene ID:7812
KEGG GENES KEGG GENES(7812)
GeneCard GeneCardCSDE1*GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links H-DBASH-DBAS G-integraG-integra cDNA-genome alignmentcDNA-genome alignment

Predicted CDS information
HIP ID HIP000335279
Predicted CDS 717..2732;  671[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.738

Motif information
ORF

length(671),orf(717:2732)
MNGQEVFYLTYTPEDVEGNVQLETGDKINFVIDNNKHTGAVSARNIMLLK
KKQARCQGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVE
FTIKDRNGKEVAPDVRLLPQGTVIFEDISIEHFEGTVTKVIPKVPSKNQN
DPLPGRIKVDFVIPKELPFGDKDTKSKVTLLEGDHVRFNISTDRRDKLER
ATNIEVLSNTFQFTNEAREMGVIAAMRDGFGFHPSVWIRECSVCSFPLPV
KFWMGTSSHIADEVEFTVVPDMLSAQRNHAIRIKKLPKGTVSFHSHSDHR
FLGTVEKEATFSNPKTTSPNKGKEKEAEDGIIAYDDCGVKLTIAFQAKDV
EGSTSPQIGDKVEFSISDKQRPGQQVATCVRLLGRNSNSKRLLGYVATLK
DNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGNKVSAE
KVNKTHSVNGITEEADPTIYSGKVIRPLRSVDPTQTEYQGMIEIVEEGDM
KGEVYPFGIVGMANKGDCLQKGESVKFQLCVLGQNAQTMAYNITPLRRAT
VECVKDQFGFINYEVGDSKKLFFHVKEVQDGIELQAGDEVEFSVILNQRT
GKCSACNVWRVCEGPKAVAAPRPDRLVNRLKNITLDDASAPRLMVLRQPR
GPDNSMGFGAERKIRQAGVID*
a.a.
length
InterPro Name
length(87), motif(38:124) 87 IPR016027 Nucleic acid-binding, OB-fold-like [Domain]
length(62), motif(55:116) 62 IPR002059 Cold-shock protein, DNA-binding [Domain]
length(62), motif(57:118) 62 IPR011129 Cold shock protein [Domain]
length(53), motif(65:117) 53 IPR012340 Nucleic acid-binding, OB-fold [Domain]
length(20), motif(67:86) 20 IPR019844 Cold-shock conserved site [Conserved_site]
length(92), motif(201:292) 92 IPR016027 Nucleic acid-binding, OB-fold-like [Domain]
length(60), motif(330:389) 60 IPR016027 Nucleic acid-binding, OB-fold-like [Domain]
length(65), motif(391:455) 65 IPR016027 Nucleic acid-binding, OB-fold-like [Domain]
length(63), motif(392:454) 63 IPR002059 Cold-shock protein, DNA-binding [Domain]
length(63), motif(393:455) 63 IPR011129 Cold shock protein [Domain]
length(53), motif(401:453) 53 IPR012340 Nucleic acid-binding, OB-fold [Domain]
length(20), motif(403:422) 20 IPR019844 Cold-shock conserved site [Conserved_site]
length(89), motif(529:617) 89 IPR016027 Nucleic acid-binding, OB-fold-like [Domain]
length(64), motif(548:611) 64 IPR011129 Cold shock protein [Domain]
length(63), motif(548:610) 63 IPR002059 Cold-shock protein, DNA-binding [Domain]
length(53), motif(556:608) 53 IPR012340 Nucleic acid-binding, OB-fold [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000001798
H-Inv cluster ID Locus viewHIX0000915
Accession number AF077054.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Similar to Cold shock domain-containing protein E1; Protein UNR; Fragment;
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (P29174)  [Identity/coverage = 100.0%/100.0%] to Cavia porcellus (Guinea pig). protein.
Experimental evidence Protein evidence
PubMed ID 1622933ALL
Gene family/group Gene family H-Inv gene family/group ID HIF0003660
Gene family/group name Cold-shock protein, DNA-binding (IPR002059).
Evidence motif (InterPro) ID IPR002059
Gene symbol/name HGNC symbol CSDE1
HGNC aliases NA
HGNC name cold shock domain containing E1, RNA-binding
DDBJ NA
UniProt CSDE1
EC number NA
GGDB
(GlycoGene Database)
Gene symbol NA
Familly NA
Designation NA
Expression NA
KEGG metabolic pathway NA
Protein-protein interaction (PPI) PPI viewer H-Inv protein ID HIP000335279
No. of interaction NA
Interaction partner(s) NA
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NM_002524NM_007158NM_001007553NM_001130523
Ensembl ENST00000261443ENST00000339438ENST00000358528ENST00000369530ENST00000369535ENST00000438362ENST00000483030ENST00000483407ENST00000524652ENST00000525132ENST00000525878ENST00000525970ENST00000529046ENST00000530784ENST00000530886ENST00000533818ENST00000534389ENST00000534699
Entrez Gene Entrez Gene ID:7812
KEGG GENES KEGG GENES(7812)
GeneCard GeneCardCSDE1*GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases
Curation status Auto-annotated
Notes NA
Related H-InvDB links Cold-shock protein, DNA-binding (IPR002059). Similarity Search ToolSimilarity Search Tool;  TACTTACT
fRNAdb (The functional RNA database) : overlapping fRNAdb entries with H-InvDB transcripts based on the location of the genome. 
NA

Gene ontology information
Molecular function DNA binding (GO:0003677);  nucleic acid binding (GO:0003676); 
Biological process regulation of transcription, DNA-dependent (GO:0006355); 

Subcellular localization information  Last modified:26-Mar-2013
WoLF PSORT nuclear; 
Target P Other
SOSUI soluble protein
TMHMM soluble protein
PTS1 Not targeted
Related H-InvDB links LIFEdb LIFEdb; 
JRE-1.4.0 or later is required. Download JRE at Sun's web site.

Protein structure information (GTOP) GTOP Last modified:26-Mar-2013
Start End PDB_ID E-value Identity Coverage SCOP_ID
15 90 1wfqA 1e-15 98.7 76/89 b.40.4.5
149 217 1wfqA 7e-10 30.4 69/89 b.40.4.5
486 549 1wfqA 5e-08 28.1 64/89 b.40.4.5
641 716 1wfqA 5e-08 28.6 74/89 b.40.4.5
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:26-Mar-2013
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator
AceGene AGhsC041102; 
Affymetrix
GeneChip
HG-Focus 219939_s_at; 
HG-U133 219939_s_at;  222975_s_at; 
HG-U133A 219939_s_at; 
HG-U133A_2 219939_s_at; 
HG-U133B 222975_s_at; 
HG-U133_Plus_2 219939_s_at;  222975_s_at; 
HG-U95 NA
HG-U95A NA
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2352973;  2352983;  2429281;  2429282;  2429283;  2429290;  2429293;  2429298;  2429301;  2429302;  2429303;  2429304;  2429306;  2429307;  2429308;  2429309;  2429310;  2429311;  2429312;  2429313;  2429318;  2429320;  2429321;  2429325;  2429326;  2429327; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 A_24_P51485; 
Related H-InvDB links H-ANGELH-ANGEL DNAProbeLocatorDNAProbeLocator

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:26-Mar-2013
Disease relation Disease name:NA
Related information in OMIM OMIM ID:NA Title:NA
Co-localized orphan diseases OMIM ID:  115665116600155600600975605225605606606788606852606928607317607671608543608553608995610320612367612596
Disease related mutation
JRE-1.4.0 or later is required.Download JRE at Sun's web site.
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(7812)
Disease Entrez Gene ID:(7812)
Substance Entrez Gene ID:(7812)
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo ViewerLEGENDALEGENDA

Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information  VaryGene Repeat mask viewer
 Single Nucleotide Polymorphism (SNP) and indel  VaryGene
Location Variation dbSNP ID Strand CDS/UTR Translation
60 .. 60 C/T rs41274132 - 5'UTR
107 .. 107 T/A rs11558870 + 5'UTR
156 .. 156 A/G rs6687539 - 5'UTR
328 .. 328 T/- rs35301858 - 5'UTR
783 .. 783 G/C rs11558868 + CDS Nonsynonymous[Gly23Arg]
1084 .. 1084 G/T rs6696347 - CDS Nonsynonymous[Ser123Ile]
1638 .. 1638 A/G rs78302744 - CDS Nonsynonymous[Arg308Gly]
2153 .. 2153 G/A rs13990 + CDS Synonymous[Glu479Glu]
2300 .. 2300 A/G rs75427731 - CDS Synonymous[Pro528Pro]
2432 .. 2432 T/C rs72994458 - CDS Synonymous[Leu572Leu]
2741 .. 2741 C/A rs9724612 + 3'UTR
2760 .. 2760 C/A rs1801909 + 3'UTR
2879 .. 2879 C/G rs6851 - 3'UTR
2940 ^ 2941 -/G rs36070559 - 3'UTR
3086 .. 3086 T/G rs74562456 - 3'UTR
3505 .. 3505 A/T rs116524200 - 3'UTR
 Microsatellite (Short Tandem Repeat, STR)
No data available
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
No data available
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD)
Related H-InvDB links VaryGeneVaryGene Repeat mask viewerRepeat Mask Viewer