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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000029398 Accession number: BC000163 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Vimentin;
 
 

Transcript original information
Accession number BC000163.2
CAGE tag ID NA
EST ID NA
Clone Number MGC:5062 IMAGE:2985712
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (VIM) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (VIM);
Sequence data provider Provider:MGC/NCI
Annotation project H-Invitational FLcDNA
Length of cDNA 1862[bp] (No. of exon:9)[A:504 T:366 G:467 C:525]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Cervix, carcinoma
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 1848(+) Signal: 1827-1831(+)
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) NA
Transcript quality feature Truncation; 
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0008682
Genomic location  G-integra Help Chromosome 10
Location 10p13
Position 17271298- 17279592
Strand +
Possible duplicated location(s) NA
Gene structure 9 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:7431
KEGG GENES KEGG GENES(7431)
GeneCard GeneCardVIM*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 HIP000104161
Predicted CDS 125..1525;  466[aa];  Orientation:+2; 
Codon Adaptation Index (CAI). 0.809
Database links RefSeq NP_003371
UniProt P08670
CCDS CCDS7120

Motif information
ORF

length(466),orf(125:1525)
MSTRSVSSSSYRRMFGGPGTASRPSSSRSYVTTSTRTYSLGSALRPSTSR
SLYASSPGGVYATRSSAVRLRSSVPGVRLLQDSVDFSLADAINTEFKNTR
TNEKVELQELNDRFANYIDKVRFLEQQNKILLAELEQLKGQGKSRLGDLY
EEEMRELRRQVDQLTNDKARVEVERDNLAEDIMRLREKLQEEMLQREEAE
NTLQSFRQDVDNASLARLDLERKVESLQEEIAFLKKLHEEEIQELQAQIQ
EQHVQIDVDVSKPDLTAALRDVRQQYESVAAKNLQEAEEWYKSKFADLSE
AANRNNDALRQAKQESTEYRRQVQSLTCEVDALKGTNESLERQMREMEEN
FAVEAANYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATY
RKLLEGEESRISLPLPNFSSLNLRETNLDSLPLVDTHSKRTLLIKTVETR
DGQVINETSQHHDDLE*
a.a.
length
InterPro Name
length(460), motif(7:466) 460 IPR027699 Vimentin [Family]
length(95), motif(7:101) 95 IPR006821 Intermediate filament head, DNA-binding domain [Domain]
length(460), motif(7:466) 460 IPR001664 Intermediate filament protein [Family]
length(309), motif(102:410) 309 IPR001664 Intermediate filament protein [Family]
length(9), motif(397:405) 9 IPR018039 Intermediate filament protein, conserved site [Conserved_site]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000029398
H-Inv cluster ID Locus viewHIX0008682
Accession number BC000163.2
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Vimentin;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (P08670)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 2251132232357924728763371665346717591509469175763112437871188903212458200147020391476210614996095151640541548933415592455158468441696424317081983179246791822033618669648186919761881194519270731196088611969033220068231201761122126946021406692214654802174688022119849ALL
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 VIM
HGNC aliases NA
HGNC name vimentin
DDBJ VIM
UniProt VIM
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 HIP000104161
No. of interaction 53
Interaction partner(s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
BIND 145685;  145803;  182069;  182083;  182103;  182109;  182110;  182111;  182112;  182113;  182114;  182116;  182117;  182118;  182119;  182120;  182121;  182122;  182160;  261893;  55727; 
DIP 175826E; 
MINT MINT-2515544;  MINT-2791056;  MINT-2791154;  MINT-2791422;  MINT-2985160;  MINT-3297793;  MINT-3979536;  MINT-3979774;  MINT-3980165;  MINT-3980250;  MINT-3980267;  MINT-3980284;  MINT-3980301;  MINT-3980318;  MINT-3980335;  MINT-3980387;  MINT-3980404;  MINT-3980421;  MINT-3980438;  MINT-3980455;  MINT-3980472;  MINT-3980489;  MINT-3981118;  MINT-3981786;  MINT-48218;  MINT-48335;  MINT-48490;  MINT-48555;  MINT-48951;  MINT-49072;  MINT-49143;  MINT-49446;  MINT-49490;  MINT-50809;  MINT-51241;  MINT-51249;  MINT-63051;  MINT-63106;  MINT-63350;  MINT-63478;  MINT-63483;  MINT-63605;  MINT-63780;  MINT-64054;  MINT-64131;  MINT-64137;  MINT-64185;  MINT-64286;  MINT-64696;  MINT-64754;  MINT-64779;  MINT-64800;  MINT-64820;  MINT-64833;  MINT-64930;  MINT-64943;  MINT-64945;  MINT-64988;  MINT-65109;  MINT-65172;  MINT-65490;  MINT-65525;  MINT-65594;  MINT-65628;  MINT-65671;  MINT-65728;  MINT-65741;  MINT-65745;  MINT-65802;  MINT-65852;  MINT-65855;  MINT-65878;  MINT-66105;  MINT-66106;  MINT-66208;  MINT-66210;  MINT-66324;  MINT-66684;  MINT-66844;  MINT-66894;  MINT-67072;  MINT-67287;  MINT-67380;  MINT-67503;  MINT-67553;  MINT-67944;  MINT-7302148;  MINT-7899812;  MINT-7945693;  MINT-7947479; 
HPRD 00017;  00032;  00146;  00253;  00302;  00442;  00513;  00564;  00675;  00946;  01070;  01132;  01147;  01206;  01238;  01241;  01261;  01262;  01363;  01447;  01557;  01565;  01721;  01726;  01862;  01908;  02293;  02433;  02461;  02698;  02730;  02799;  02803;  02972;  02994;  03019;  03075;  03144;  03180;  03183;  03203;  03321;  03334;  03382;  03414;  03445;  03457;  03459;  03579;  03605;  03634;  03754;  03756;  03819;  03913;  03965;  04122;  04170;  04184;  04187;  04340;  04494;  04528;  04585;  04833;  05059;  05375;  05428;  05457;  05496;  05639;  05703;  06024;  06170;  06183;  06311;  06712;  06772;  06828;  06848;  06910;  07135;  07191;  07206;  07601;  08687;  08932;  08986;  09071;  09173;  09315;  09326;  09471;  09570;  09653;  09753;  10004;  10037;  10280;  10349;  10379;  10424;  10488;  10603;  10616;  10665;  11028;  11476;  11493;  12093;  12193;  13173;  13628;  14358;  14403;  14543;  14725;  14763;  15307;  15336;  15552;  15627;  15951;  16050;  16246;  16348;  16635;  16669;  16735;  16836;  17187;  17212;  17975;  18051;  18293;  19599; 
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:7431
KEGG GENES KEGG GENES(7431)
GeneCard GeneCardVIM*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. 
FR ID FR101428
Accession
Description
Location
PMID
FR ID FR235286
Accession
Description
Location
PMID

Gene ontology information
Molecular function structural molecule activity (GO:0005198); 
Cellular component intermediate filament (GO:0005882); 

Subcellular localization information  Last modified:27-May-2015
WoLF PSORT nuclear;  cytosol;  mitochondria; 
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.

Gene expression information  H-ANGEL DNAProbeLocator Last modified:27-May-2015
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator
AceGene AGhsA190207; 
Affymetrix
GeneChip
HG-Focus 201426_s_at; 
HG-U133 201426_s_at; 
HG-U133A 201426_s_at; 
HG-U133A_2 201426_s_at; 
HG-U133B NA
HG-U133_Plus_2 201426_s_at; 
HG-U95 34091_s_at;  55620_at;  75309_at; 
HG-U95A 34091_s_at; 
HG-U95B NA
HG-U95C 55620_at; 
HG-U95D 75309_at; 
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 3236971;  3236980;  3236987;  3236988;  3236991;  3236993;  3236995;  3236997;  3236999;  3237000;  3237001;  3237002;  3237003;  3279898;  3279900;  3279901;  3279903;  3279905;  3279906; 
HuGeneFL Z19554_s_at; 
Agilent Human 1A Oligo Microarray:PGID215 A_23_P161190; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P161190;  A_23_P161194; 
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
7 .. 7 G/A rs192867529 + 5'UTR
46 .. 46 C/T rs11545555 + 5'UTR
98 .. 98 C/T rs200253669 + 5'UTR
103 .. 103 G/C rs3758410 - 5'UTR
177 .. 177 C/T rs11545549 + CDS Nonsynonymous[Pro18Leu]
266 .. 266 A/C rs201189169 + CDS Nonsynonymous[Thr48Pro]
273 .. 273 G/A rs11545553 + CDS Nonsynonymous[Arg50His]
316 .. 316 C/A rs34171769 - CDS Synonymous[Arg64Arg]
328 .. 328 G/C rs11545547 + CDS Synonymous[Val68Val]
352 .. 352 G/T rs111616371 + CDS Synonymous[Gly76Gly]
353 .. 353 G/A rs184701100 + CDS Nonsynonymous[Val77Met]
354 .. 354 T/C rs11545548 + CDS Nonsynonymous[Val77Ala]
406 .. 406 C/T rs144539901 + CDS Synonymous[Thr94Thr]
508 .. 508 T/C rs147857896 + CDS Synonymous[Asn128Asn]
514 .. 514 C/A rs113013980 + CDS Synonymous[Ile130Ile]
520 .. 520 G/A rs11545554 + CDS Synonymous[Leu132Leu]
562 .. 562 G/A rs1042003 + CDS Synonymous[Leu146Leu]
575 .. 575 G/A rs121917775 + CDS Nonsynonymous[Glu151Lys]
578 .. 578 G/A rs141319821 + CDS Nonsynonymous[Glu152Lys]
613 .. 613 G/A rs201551781 + CDS Synonymous[Gln163Gln]
638 .. 638 G/C rs11545550 + CDS Nonsynonymous[Glu172Gln]
666 .. 666 A/C rs149942621 + CDS Nonsynonymous[Asp181Ala]
677 .. 677 C/G rs201325757 + CDS Nonsynonymous[Leu185Val]
678 .. 678 T/C rs11545551 + CDS Nonsynonymous[Leu185Pro]
723 .. 723 A/G rs145760831 + CDS Nonsynonymous[Glu200Gly]
733 .. 733 G/A rs148956484 + CDS Synonymous[Leu203Leu]
736 .. 736 A/G rs143636314 + CDS Synonymous[Gln204Gln]
754 .. 754 T/C rs61761616 + CDS Synonymous[Val210Val]
759 .. 759 A/G rs116800063 + CDS Nonsynonymous[Asn212Ser]
770 .. 770 G/A rs138235394 + CDS Nonsynonymous[Ala216Thr]
838 .. 838 C/T rs141244457 + CDS Synonymous[His238His]
873 .. 873 A/G rs145152785 + CDS Nonsynonymous[Gln250Arg]
890 .. 890 A/G rs139037306 + CDS Nonsynonymous[Ile256Val]
898 .. 898 G/A rs141519986 + CDS Synonymous[Val258Val]
920 .. 920 A/G rs113576905 + CDS Nonsynonymous[Thr266Ala]
921 .. 921 C/T rs150878383 + CDS Nonsynonymous[Thr266Met]
922 .. 922 G/A rs137961338 + CDS Synonymous[Thr266Thr]
937 .. 937 C/T rs4903 + CDS Synonymous[Asp271Asp]
938 .. 938 G/A rs199515026 + CDS Nonsynonymous[Val272Ile]
962 .. 962 G/T rs147133187 + CDS Nonsynonymous[Ala280Ser]
1003 .. 1003 C/G rs11254467 + CDS Synonymous[Ser293Ser]
1023 .. 1023 A/G rs144238562 + CDS Nonsynonymous[Glu300Gly]
1046 .. 1046 G/T rs11545546 + CDS Nonsynonymous[Ala308Ser]
1111 .. 1111 A/G rs147429387 + CDS Synonymous[Glu329Glu]
1118 .. 1118 G/A rs200772352 + CDS Nonsynonymous[Ala332Thr]
1132 .. 1132 C/T rs111932484 + CDS Synonymous[Thr336Thr]
1158 .. 1158 G/A rs116370722 + CDS Nonsynonymous[Arg345His]
1175 .. 1175 T/G rs200740172 + CDS Nonsynonymous[Phe351Val]
1204 .. 1204 C/G rs139818786 + CDS Nonsynonymous[Asp360Glu]
1209 .. 1209 T/C rs114322672 + CDS Nonsynonymous[Ile362Thr]
1216 .. 1216 C/G rs116696668 + CDS Synonymous[Arg364Arg]
1256 .. 1256 C/T rs201530534 + CDS Nonsynonymous[Arg378Cys]
1266 .. 1266 G/A rs35157876 - CDS Nonsynonymous[Arg381His]
1345 .. 1345 G/A rs150986868 + CDS Synonymous[Glu407Glu]
1371 .. 1371 C/A rs11545541 - CDS Nonsynonymous[Pro416Gln]
1381 .. 1381 C/T rs11545556 + CDS Synonymous[Ser419Ser]
1390 .. 1390 C/T rs140482660 + CDS Synonymous[Asn422Asn]
1417 .. 1417 C/T rs150003485 + CDS Synonymous[Leu431Leu]
1424 .. 1424 G/A rs146586974 + CDS Nonsynonymous[Val434Ile]
1509 .. 1509 A/C rs11545543 - CDS Nonsynonymous[His462Pro]
1537 .. 1537 A/T rs144519674 + 3'UTR
1580 .. 1580 C/T rs12667 + 3'UTR
1632 .. 1632 G/A rs112279926 + 3'UTR
1654 .. 1654 A/G rs9235 + 3'UTR
1661 .. 1661 C/G rs186277663 + 3'UTR
1667 .. 1667 C/G/T rs9059 + 3'UTR
1671 .. 1671 A/T rs189996263 + 3'UTR
1672 .. 1672 C/G/T rs9486 + 3'UTR
1687 .. 1687 C/T rs9485 + 3'UTR
1697 ^ 1698 -/A rs71683678 + 3'UTR
1720 .. 1720 G/T rs9484 + 3'UTR
1753 .. 1753 T/C rs11545542 - 3'UTR
1772 .. 1772 C/T rs3249 - 3'UTR
1784 .. 1784 T/- rs71724273 + 3'UTR
1817 .. 1817 G/T rs1049341 - 3'UTR
1820 .. 1820 C/T rs1063520 + 3'UTR
1847 .. 1847 C/A rs3179873 + 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