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: 20-Apr-2012
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 ENST00000313766;  ENST00000471328;  ENST00000477004;  ENST00000512382;  ENST00000515795; 
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 12690205;  12853948;  15489334;  15676076;  17924334;  17974005;  19159218;  ALL; 
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 5
Interaction partner(s) HIP000034909;  HIP000058989;  HIP000070686;  HIP000089951;  HIP000093088; 
BIND NA
DIP NA
MINT NA
HPRD 01348;  01742;  02436;  16246; 
IntAct EBI-2876884;  EBI-2849041;  EBI-2854244;  EBI-2853878;  EBI-2850398; 
Database links RefSeq NM_020223; 
Ensembl ENST00000313766;  ENST00000471328;  ENST00000477004;  ENST00000512382;  ENST00000515795; 
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:20-Apr-2012
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:20-Apr-2012
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:20-Apr-2012
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 Viewer;  LEGENDALEGENDA; 

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;