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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000056966 Accession number: BX648319 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Protein SDE2 homolog;
 
 

Transcript original information
Accession number BX648319.1
CAGE tag ID NA
EST ID NA
Clone Number DKFZp686O02131
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (SDE2) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (SDE2);
Sequence data provider Provider:DKFZ/MIPS
Annotation project H-Invitational FLcDNA
Length of cDNA 3987[bp] (No. of exon:7)[A:1053 T:1306 G:871 C:757]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type human uterus
Develpmental stage adult
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 3967(+) Signal: 3940-3944(+)
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) NA
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0001641
Genomic location  G-integra Help Chromosome 1
Location 1q42.12
Position 226170403- 226187023
Strand -
Possible duplicated location(s) NA
Gene structure 7 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:163859
KEGG GENES KEGG GENES(163859)
GeneCard GeneCardSDE2*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 HIP000025217
Predicted CDS 12..1367;  451[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.742

Motif information
ORF

length(451),orf(12:1367)
MAEAAALVWIRGPGFGCKAVRCASGRCTVRDFIHRHCQDQNVPVENFFVK
CNGALINTSDTVQHGAVYSLEPRLCGGKGGFGSMLRALGAQIEKTTNREA
CRDLSGRRLRDVNHEKAMAEWVKQQAEREAEKEQKRLERLQRKLVEPKHC
FTSPDYQQQCHEMAERLEDSVLKGMQAASSKMVSAEISENRKRQWPTKSQ
TDRGASAGKRRCFWLGMEGLETAEGSNSESSDDDSEEAPSTSGMGFHAPK
IGSNGVEMAAKFPSGSQRARVVNTDHGSPEQLQIPVTDSGRHILEDSCAE
LGESKEHMESRMVTETEETQEKKAESKEPIEEEPTGAGLNKDKETEERTD
GERVAEVAPEERENVAVAKLQESQPGIAVIDKETIDLLAFTSVAELELLG
LEKLKCELMALGLKCGGTLQERAARLFSVRGLAKEQIDPALFAKPLKGKK
K*
a.a.
length
InterPro Name
length(103), motif(64:166) 103 IPR024974 Sde2 N-terminal domain [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000056966
H-Inv cluster ID Locus viewHIX0001641
Accession number BX648319.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Protein SDE2 homolog;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (Q6IQ49)  [Identity/coverage = 99.778%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 147020391548933416710414175253321822033618669648196903322006823121269460ALL
Gene family/group Gene family H-Inv gene family/group ID NA
Gene family/group name NA
Evidence motif (InterPro) ID NA
Gene symbol/name HGNC symbol SDE2
HGNC aliases "chromosome 1 open reading frame 55"
HGNC name SDE2 telomere maintenance homolog (S. pombe)
DDBJ NA
UniProt SDE2
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 HIP000025217
No. of interaction 64
Interaction partner(s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
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:163859
KEGG GENES KEGG GENES(163859)
GeneCard GeneCardSDE2*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 Gene familyGene family;  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


Subcellular localization information  Last modified:27-May-2015
WoLF PSORT mitochondria;  cytosol;  endoplasmic;  Other; 
Target P Not predicted
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:27-May-2015
Start End PDB_ID E-value Identity Coverage SCOP_ID
28 77 1aarA 2e-04 20.0 50/100 d.15.1.1
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:27-May-2015
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator
AceGene AGhsB101101; 
Affymetrix
GeneChip
HG-Focus NA
HG-U133 244103_at; 
HG-U133A NA
HG-U133A_2 NA
HG-U133B 244103_at; 
HG-U133_Plus_2 1553338_at;  244103_at; 
HG-U95 57447_at; 
HG-U95A NA
HG-U95B 57447_at; 
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2383043;  2383045;  2383049;  2383051;  2458650;  2458651;  2458652;  2458654;  2458655;  2458656;  2458657;  2458658;  2458659;  2458660;  2458661;  2458662;  2458663;  2458665; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 A_23_P159144;  A_23_P304410; 
Whole Human Genome Oligo Microarray:PGID247 A_32_P64475; 
Related H-InvDB links H-ANGELH-ANGEL DNAProbeLocatorDNAProbeLocator

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
32 .. 32 G/C rs199904241 - CDS Synonymous[Leu7Leu]
47 .. 47 C/T rs201347746 - CDS Synonymous[Gly12Gly]
49 .. 49 C/T rs150202613 - CDS Nonsynonymous[Pro13Leu]
78 .. 78 G/T rs200698120 - CDS Nonsynonymous[Ala23Ser]
83 .. 83 G/A rs201120938 - CDS Synonymous[Ser24Ser]
140 .. 140 A/T rs200918535 - CDS Synonymous[Pro43Pro]
361 .. 361 C/T rs200982731 - CDS Nonsynonymous[Ala117Val]
395 .. 395 A/G rs184898819 - CDS Synonymous[Arg128Arg]
403 .. 403 A/G rs199840109 - CDS Nonsynonymous[Glu131Gly]
444 .. 444 G/A rs200329712 - CDS Nonsynonymous[Val145Ile]
632 .. 632 G/A rs202100514 - CDS Synonymous[Ala207Ala]
712 .. 712 A/G rs199998745 - CDS Nonsynonymous[Asp234Gly]
775 .. 775 G/A rs141939942 - CDS Nonsynonymous[Gly255Asp]
779 .. 779 C/T rs200328355 - CDS Synonymous[Val256Val]
780 .. 780 G/A rs182179659 - CDS Nonsynonymous[Glu257Lys]
838 .. 838 A/G rs41268719 - CDS Nonsynonymous[His276Arg]
897 .. 897 G/T rs61998244 - CDS Nonsynonymous[Asp296Tyr]
947 .. 947 G/T rs34348128 - CDS Nonsynonymous[Met312Ile]
952 .. 952 C/T rs61731742 - CDS Nonsynonymous[Thr314Ile]
979 .. 979 A/C rs113721886 - CDS Nonsynonymous[Lys323Thr]
999 .. 999 A/G rs112422303 - CDS Nonsynonymous[Ile330Val]
1012 .. 1012 C/G rs190593519 - CDS Nonsynonymous[Pro334Arg]
1103 .. 1103 C/T rs201203772 - CDS Synonymous[Asn364Asn]
1153 .. 1153 A/G rs76285584 - CDS Nonsynonymous[Asp381Gly]
1168 .. 1168 A/G rs184725920 - CDS Nonsynonymous[Asp386Gly]
1178 .. 1178 G/A rs201730097 - CDS Synonymous[Ala389Ala]
1203 .. 1203 T/A rs193190607 - CDS Nonsynonymous[Leu398Met]
1217 .. 1217 G/A rs200116300 - CDS Synonymous[Glu402Glu]
1327 .. 1327 C/T rs74756813 - CDS Nonsynonymous[Pro439Leu]
1406 .. 1406 A/G rs200544214 - 3'UTR
1641 .. 1641 T/A rs147593112 - 3'UTR
1767 .. 1767 G/A rs76843836 - 3'UTR
1807 .. 1807 G/T rs142542568 - 3'UTR
1808 .. 1808 G/T rs184242613 - 3'UTR
1890 .. 1890 G/A rs149192547 - 3'UTR
1935 .. 1935 G/A rs145378495 - 3'UTR
1947 .. 1947 T/C rs61835211 - 3'UTR
1967 .. 1967 C/A rs61835210 - 3'UTR
1981 .. 1981 A/G rs150033284 - 3'UTR
2062 .. 2062 C/T rs192567859 - 3'UTR
2063 .. 2063 G/A rs187567406 - 3'UTR
2125 .. 2125 G/A rs182862864 - 3'UTR
2147 .. 2147 A/G rs116049995 - 3'UTR
2149 .. 2149 A/G rs116538901 - 3'UTR
2192 .. 2192 T/G rs146386773 - 3'UTR
2198 .. 2198 A/G rs143612910 - 3'UTR
2210 .. 2210 T/G rs71646758 - 3'UTR
2378 .. 2378 G/C rs115533329 - 3'UTR
2390 .. 2390 T/C rs192301222 - 3'UTR
2435 .. 2435 G/A rs140005759 - 3'UTR
2453 .. 2453 A/G rs150643022 - 3'UTR
2460 .. 2460 A/G rs141866182 - 3'UTR
2570 .. 2570 A/G rs2755101 - 3'UTR
2599 .. 2599 T/A rs188419824 - 3'UTR
2600 .. 2600 T/C rs182914314 - 3'UTR
2657 .. 2657 G/C rs111766307 - 3'UTR
2680 .. 2680 C/T rs144568055 - 3'UTR
2708 .. 2708 G/A rs142795418 - 3'UTR
2719 .. 2719 A/T rs138953356 - 3'UTR
2865 .. 2865 G/T rs146091318 - 3'UTR
2877 .. 2877 C/T rs190738824 - 3'UTR
2895 .. 2895 C/G rs6664468 - 3'UTR
3045 .. 3045 G/A rs74148409 - 3'UTR
3067 .. 3067 C/T rs76220707 - 3'UTR
3282 .. 3282 A/G rs117173944 - 3'UTR
3309 .. 3309 T/G rs186169822 - 3'UTR
3359 .. 3359 A/G rs137859180 - 3'UTR
3585 .. 3585 A/G rs150296379 - 3'UTR
3589 .. 3589 A/G rs182896360 - 3'UTR
3696 .. 3696 T/A rs140237187 - 3'UTR
3789 .. 3789 G/A rs191058439 - 3'UTR
3859 .. 3859 T/C rs187180320 - 3'UTR
3873 .. 3873 G/A rs181060320 - 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
Type Start End Strand
L1MEf 1516 1837 -
AluY 1838 2140 -
L1MEf 2141 2400 -
AluSq2 2401 2704 -
L1MEf 2705 2965 -
FLAM_C 2966 3114 +
L1MEf 3115 3570 -
L1MEf 3638 3967 -
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD)
Related H-InvDB links VaryGeneVaryGene Repeat mask viewerRepeat Mask Viewer