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: HIT000026389 Accession number: AL390147 Created date: 26-Mar-2013 Last modified: 26-Mar-2013
Definition: Similar to Dentin matrix protein 4; DMP-4; Protein FAM20C; Precursor;
 
 

Transcript original information
Accession number AL390147.1
CAGE tag ID NA
EST ID NA
Clone Number DKFZp547D065
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (FAM20C) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (FAM20C);
Sequence data provider Provider:DKFZ/MIPS
Annotation project H-Invitational FLcDNA
Length of cDNA 2195[bp] (No. of exon:7)[A:447 T:412 G:695 C:641]
Devision HTC
Molecular type mRNA
Library origin Cell type NA
Tissue type brain
Develpmental stage fetal
Mini-G
Sequence quality information
CDS feature N-truncated
Kozak sequence NA
PolyA Site: 2178(+) Signal: 2157-2161(+)
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) NA
Transcript quality feature NA
Notes UM gene supported by high quality evidences.

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0019573
Genomic location  G-integra Help Chromosome 7
Location 7p22.3
Position 285861- 300711
Strand +
Possible duplicated location(s) NA
Gene structure 7 exon(s)
Database links RefSeq NM_020223
Ensembl ENST00000313766ENST00000471328ENST00000477004ENST00000512382ENST00000515795
Entrez Gene Entrez Gene ID:56975
KEGG GENES KEGG GENES(56975)
GeneCard GeneCardFAM20C*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 HIP000012434
Predicted CDS 351..1412;  353[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.855

Motif information
ORF

length(353),orf(351:1412)
GPVGSWVPRVPKAQGGPEEAGAPPHFSYEEPSTSRLPPAPGGFLSDKPFL
FLSCFLRQTREQETPPDFFYFSDYERHNAEIAAFHLDRILDFRRVPPVAG
RMVNMTKEIRDVTRDKKLWRTFFISPANNICFYGECSYYCSTEHALCGKP
DQIEGSLAAFLPDLSLAKRKTWRNPWRRSYHKRKKAEWEVDPDYCEEVKQ
TPPYDSSHRILDVMDMTIFDFLMGNMDRHHYETFEKFGNETFIIHLDNGR
GFGKYSHDELSILVPLQQCCRIRKSTYLRLQLLAKEEYKLSLLMAESLRG
DQVAPVLYQPHLEALDRRLRVVLKAVRDCVERDGLHSVVDDDLDTEHRAA
SAR*
a.a.
length
InterPro Name
length(281), motif(57:337) 281 IPR009581 Protein of unknown function DUF1193 [Family]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000026389
H-Inv cluster ID Locus viewHIX0019573
Accession number AL390147.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Similar to Dentin matrix protein 4; DMP-4; Protein FAM20C; Precursor;
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (Q8IXL6)  [Identity/coverage = 98.993%/51.03%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 12690205128539481548933415676076179243341797400519159218ALL
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 FAM20C
HGNC aliases NA
HGNC name family with sequence similarity 20, member C
DDBJ DKFZp547D065
UniProt FAM20C
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 HIP000012434
No. of interaction NA
Interaction partner(s) NA
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NM_020223
Ensembl ENST00000313766ENST00000471328ENST00000477004ENST00000512382ENST00000515795
Entrez Gene Entrez Gene ID:56975
KEGG GENES KEGG GENES(56975)
GeneCard GeneCardFAM20C*GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases
Curation status Auto-annotated
Notes UM gene supported by high quality evidences.
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:26-Mar-2013
WoLF PSORT nuclear;  cytosol; 
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:26-Mar-2013
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator
AceGene AGhsB260913; 
Affymetrix
GeneChip
HG-Focus NA
HG-U133 226722_at; 
HG-U133A NA
HG-U133A_2 NA
HG-U133B 226722_at; 
HG-U133_Plus_2 226722_at; 
HG-U95 72964_at;  90257_at; 
HG-U95A NA
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E 72964_at;  90257_at; 
HG-U95Av2 NA
HuEx-1_0 NA
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 A_23_P250122; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P250122; 
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:  605635
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:(56975)
Disease Entrez Gene ID:(56975)
Substance Entrez Gene ID:(56975)
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
563 .. 563 C/T rs11546478 + CDS Synonymous[Phe71Phe]
1316 .. 1316 T/G rs36170987 + CDS Synonymous[Val322Val]
1329 .. 1329 C/T rs62644536 + CDS Nonsynonymous[Arg327Trp]
1334 .. 1334 C/T rs11546480 + CDS Synonymous[Asp328Asp]
1347 .. 1347 G/A rs36139924 + CDS Nonsynonymous[Asp333Asn]
1442 .. 1442 A/G rs36173075 + 3'UTR
1453 .. 1453 G/C rs36138803 + 3'UTR
1482 .. 1482 C/T rs11546477 + 3'UTR
1647 .. 1647 G/A rs11546481 + 3'UTR
1978 .. 1978 G/A rs11546479 + 3'UTR
1979 .. 1979 C/T rs1134015 + 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