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: HIT000000610 Accession number: AB020700 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: WD repeat-containing protein 47 isoform 3.
 
 

Transcript original information
Accession number AB020700.1
CAGE tag ID NA
EST ID NA
Clone Number hk08702
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (WDR47) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (WDR47);
Sequence data provider Provider:KDRI; 
Annotation project H-Invitational FLcDNA
Length of cDNA 4195[bp] (No. of exon:15)[A:1205 T:1232 G:922 C:836]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type brain
Develpmental stage adult
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA NA
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) AAGAAG; 
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0199788
Genomic location  G-integra Help Chromosome 1
Location NA
Position 109512840- 109584697
Strand -
Possible duplicated location(s) NA
Gene structure 15 exon(s)
Database links RefSeq NM_014969;  NM_001142550;  NM_001142551; 
Ensembl ENST00000357672;  ENST00000361054;  ENST00000369962;  ENST00000369965;  ENST00000400794;  ENST00000528747;  ENST00000529074;  ENST00000530772;  ENST00000531337; 
Entrez Gene Entrez Gene ID:22911; 
KEGG GENES KEGG GENES(22911); 
GeneCard GeneCardWDR47;  *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 HIP000105298
Predicted CDS 224..2983;  919[aa];  Orientation:+2; 
Codon Adaptation Index (CAI). 0.697
Database links RefSeq NP_001136023; 
UniProt O94967; 
CCDS CCDS44187; 

Motif information
ORF

length(919),orf(224:2983) MTAEETVNVKEVEIIKLILDFLNSKKLHISMLALEKESGVINGLFSDDML FLRQLILDGQWDEVLQFIQPLECMEKFDKKRFRYIILKQKFLEALCVNNA MSAEDEPQHLEFTMQEAVQCLHALEEYCPSKDDYSKLCLLLTLPRLTNHA EFKDWNPSTARVHCFEEACVMVAEFIPADRKLSEAGFKASNNRLFQLVMK GLLYECCVEFCQSKATGEEITESEVLLGIDLLCGNGCDDLDLSLLSWLQN LPSSVFSCAFEQKMLNIHVDKLLKPTKAAYADLLTPLISKLSPYPSSPMR RPQSADAYMTRSLNPALDGLTCGLTSHDKRISDLGNKTSPMSHSFANFHY PGVQNLSRSLMLENTECHSIYEESPERDTPVDAQRPIGSEILGQSSVSEK EPANGAQNPGPAKQEKNELRDSTEQFQEYYRQRLRYQQHLEQKEQQRQIY QQMLLEGGVNQEDGPDQQQNLTEQFLNRSIQKLGELNIGMDGLGNEVSAL NQQCNGSKGNGSNGSSVTSFTTPPQDSSQRLTHDASNIHTSTPRNPGSTN HIPFLEESPCGSQISSEHSVIKPPLGDSPGSLSRSKGEEDDKSKKQFVCI NILEDTQAVRAVAFHPAGGLYAVGSNSKTLRVCAYPDVIDPSAHETPKQP VVRFKRNKHHKGSIYCVAWSPCGQLLATGSNDKYVKVLPFNAETCNATGP DLEFSMHDGTIRDLAFMEGPESGGAILISAGAGDCNIYTTDCQRGQGLHA LSGHTGHILALYTWSGWMIASGSQDKTVRFWDLRVPSCVRVVGTTFHGTG SAVASVAVDPSGRLLATGQEDSSCMLYDIRGGRMVQSYHPHSSDVRSVRF SPGAHYLLTGSYDMKIKVTDLQGDLTKQLPIMVVGEHKDKVIQCRWHTQD LSFLSSSADRTVTLWTYNG* 		a.a.
length		 InterPro Name
length(33), motif(10:42) 33 IPR006594 LisH dimerisation motif [Domain]
length(58), motif(45:102) 58 IPR006595 CTLH, C-terminal LisH motif [Domain]
length(39), motif(596:634) 39 IPR001680 WD40 repeat [Repeat]
length(315), motif(604:918) 315 IPR015943 WD40/YVTN repeat-like-containing domain [Domain]
length(27), motif(606:632) 27 IPR019781 WD40 repeat, subgroup [Repeat]
length(311), motif(606:916) 311 IPR011046 WD40 repeat-like-containing domain [Domain]
length(43), motif(647:689) 43 IPR001680 WD40 repeat [Repeat]
length(31), motif(657:687) 31 IPR019782 WD40 repeat 2 [Repeat]
length(263), motif(657:919) 263 IPR017986 WD40-repeat-containing domain [Domain]
length(30), motif(658:687) 30 IPR019781 WD40 repeat, subgroup [Repeat]
length(45), motif(697:741) 45 IPR001680 WD40 repeat [Repeat]
length(39), motif(744:782) 39 IPR001680 WD40 repeat [Repeat]
length(37), motif(746:782) 37 IPR019781 WD40 repeat, subgroup [Repeat]
length(41), motif(751:791) 41 IPR019782 WD40 repeat 2 [Repeat]
length(15), motif(769:783) 15 IPR019775 WD40 repeat, conserved site [Conserved_site]
length(40), motif(789:828) 40 IPR001680 WD40 repeat [Repeat]
length(35), motif(794:828) 35 IPR019781 WD40 repeat, subgroup [Repeat]
length(42), motif(796:837) 42 IPR019782 WD40 repeat 2 [Repeat]
length(40), motif(831:870) 40 IPR001680 WD40 repeat [Repeat]
length(34), motif(835:868) 34 IPR019781 WD40 repeat, subgroup [Repeat]
length(35), motif(838:872) 35 IPR019782 WD40 repeat 2 [Repeat]
length(40), motif(877:916) 40 IPR001680 WD40 repeat [Repeat]
length(35), motif(881:915) 35 IPR019781 WD40 repeat, subgroup [Repeat]
length(36), motif(884:919) 36 IPR019782 WD40 repeat 2 [Repeat]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000000610
H-Inv cluster ID Locus viewHIX0199788
Accession number AB020700.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help Representative H-Inv IDRepresentative transcript;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition WD repeat-containing protein 47 isoform 3.
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (NP_001136023)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens protein.
Experimental evidence Protein evidence
PubMed ID NA
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 WDR47
HGNC aliases NA
HGNC name WD repeat domain 47
DDBJ KIAA0893
UniProt NA
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 HIP000105298
No. of interaction 12
Interaction partner(s) HIP000030585;  HIP000033190;  HIP000039383;  HIP000039653;  HIP000060275;  HIP000071861;  HIP000076344;  HIP000083959;  HIP000096070;  HIP000100267;  HIP000192629;  HIP000333923; 
BIND NA
DIP NA
MINT MINT-6488791;  MINT-7945693; 
HPRD 01475;  03590;  04155;  05923;  07411;  09732;  11822;  11906;  11907;  11909;  11912;  13626;  16059; 
IntAct EBI-2880601;  EBI-2880211;  EBI-1237540;  EBI-3962281; 
Database links RefSeq NM_014969;  NM_001142550;  NM_001142551; 
Ensembl ENST00000357672;  ENST00000361054;  ENST00000369962;  ENST00000369965;  ENST00000400794;  ENST00000528747;  ENST00000529074;  ENST00000530772;  ENST00000531337; 
Entrez Gene Entrez Gene ID:22911; 
KEGG GENES KEGG GENES(22911); 
GeneCard GeneCardWDR47;  *GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases; 
Curation status Human curated
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:20-Apr-2012
WoLF PSORT nuclear;  cytosol; 
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:20-Apr-2012
Start End PDB_ID E-value Identity Coverage SCOP_ID
13 76 1uujA 3e-11 19.7 61/76 a.221.1.1
594 915 1nr0A1 4e-29 16.2 296/311 b.69.4.1
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:20-Apr-2012
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator		 AceGene AGhsA240912; 
Affymetrix
GeneChip		 HG-Focus NA
HG-U133 203855_at; 
HG-U133A 203855_at; 
HG-U133A_2 203855_at; 
HG-U133B NA
HG-U133_Plus_2 203855_at; 
HG-U95 35720_at; 
HG-U95A 35720_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2350464;  2426841;  2426842;  2426843;  2426844;  2426846;  2426848;  2426849;  2426850;  2426852;  2426854;  2426857;  2426858;  2426859;  2426860;  2426861;  2426862;  2426863;  2426865;  4052652;  4052654;  4052678;  4052680;  4052682;  4054126;  4054127;  4054132;  4054133; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 A_23_P23748; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P23748; 
Related H-InvDB links H-ANGELH-ANGEL;  DNAProbeLocatorDNAProbeLocator; 

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:20-Apr-2012
Disease relation Disease name:NA
Related information in OMIM OMIM ID:NA Title:NA
Co-localized orphan diseases OMIM ID:  115665;  116600;  155600;  600975;  605225;  605606;  606788;  606852;  606928;  607317;  607671;  608543;  608553;  608995;  610320;  612367;  612596; 
Disease related mutation NA
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(22911)
Disease Entrez Gene ID:(22911)
Substance Entrez Gene ID:(22911)
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo Viewer;  LEGENDALEGENDA; 

Evolutionary information  Evola Help Last modified:20-Apr-2012
Relationship Species Accession number MGI Links
Orthology Mus sp. (Mouse) BC040337 MGI:2139593 G-integraG-integra
Orthology Macaca sp. (Macaque) ENSMMUT00000012951 G-integraG-integra
Orthology Oryzias sp. (Medaka) ENSORLT00000008618 G-integraG-integra
Orthology Oryzias sp. (Medaka) ENSORLT00000019622 G-integraG-integra
Orthology Pongo sp. (Orangutan) ENSPPYT00000001301 G-integraG-integra
Orthology Pan sp. (Chimpanzee) ENSPTRT00000001956 G-integraG-integra
Orthology Tetraodon sp. (Tetraodon) GSTENT00028473001 G-integraG-integra
Orthology Takifugu sp. (Fugu) SINFRUT00000160446 G-integraG-integra
Orthology Takifugu sp. (Fugu) SINFRUT00000166078 G-integraG-integra
Orthology Bos sp. (Cow) XM_001253082 G-integraG-integra
Orthology Monodelphis sp. (Opossum) XM_001381894 G-integraG-integra
Orthology Equus sp. (Horse) XM_001493773 G-integraG-integra
Orthology Danio sp. (Zebrafish) XM_001922584 G-integraG-integra
Orthology Gallus sp. (Chicken) XM_422187 G-integraG-integra
Orthology Canis sp. (Dog) XM_547247 G-integraG-integra
Phylogenetic tree [View by ATV]
 Neighbor-joining (phb) 
Related H-InvDB links EvolaEvola;  dN/dS (under constraction); 

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
422 .. 422 T/C rs112410635 - CDS Nonsynonymous[Phe67Leu]
482 .. 482 C/T rs55730953 - CDS Synonymous[Leu87Leu]
1392 .. 1392 A/G rs79997809 - CDS Nonsynonymous[Glu390Gly]
1827 .. 1827 C/T rs113434051 - CDS Nonsynonymous[Ala535Val]
2080 .. 2080 T/C rs41299563 - CDS Synonymous[Gly619Gly]
2429 .. 2429 A/C rs1538137 - CDS Nonsynonymous[Asn736His]
2443 .. 2443 C/T rs76370963 - CDS Synonymous[Thr740Thr]
2481 .. 2481 G/T rs74576781 - CDS Nonsynonymous[Gly753Val]
2778 ^ 2779 -/C rs35988108 - CDS
3345 .. 3345 T/G rs112609892 - 3'UTR
3538 .. 3538 A/G rs507776 - 3'UTR
3756 .. 3756 T/A rs114053618 - 3'UTR
3761 .. 3761 T/C rs11803800 - 3'UTR
4181 .. 4181 G/C rs12068536 - 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;