H-InvDB x AHG DB
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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000026389 Accession number: AL390147 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Similar to Extracellular serine/threonine protein kinase FAM20C; EC=2.7.11.1; Dentin matrix protein 4; DMP-4; Golgi-enriched fraction casein kinase; GEF-CK; 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 NA
Ensembl NA
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). 0.841

Motif information
ORF

length(353),orf(351:1412)
GPVGSWVPRVPKAQGGPEEAGAPPHFSYEEPSTSRLPPAPGGFLSDKPFL
FLSCFLRQTREQETPPDFFYFSDYERHNAEIAAFHLDRILDFRRVPPVAG
RMVNMTKEIRDVTRDKKLWRTFFISPANNICFYGECSYYCSTEHALCGKP
DQIEGSLAAFLPDLSLAKRKTWRNPWRRSYHKRKKAEWEVDPDYCEEVKQ
TPPYDSSHRILDVMDMTIFDFLMGNMDRHHYETFEKFGNETFIIHLDNGR
GFGKYSHDELSILVPLQQCCRIRKSTYLRLQLLAKEEYKLSLLMAESLRG
DQVAPVLYQPHLEALDRRLRVVLKAVRDCVERDGLHSVVDDDLDTEHRAA
SAR*
a.a.
length
InterPro Name
length(298), motif(56:353) 298 IPR024869 FAM20 [Family]
length(221), motif(122:342) 221 IPR009581 Domain of unknown function DUF1193 [Domain]

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 Extracellular serine/threonine protein kinase FAM20C; EC=2.7.11.1; Dentin matrix protein 4; DMP-4; Golgi-enriched fraction casein kinase; GEF-CK; 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 1269020512853948154893341567607617924334179740051915921822582013ALL
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 EC 2.7.11.1non-specific serine/threonine protein kinase; 
GGDB
(GlycoGene Database)
Gene symbol NA
Familly NA
Designation NA
Expression NA
KEGG metabolic pathway 04150 :mTOR signaling pathway;  04210 :Apoptosis;  04310 :Wnt signaling pathway;  04320 :Dorso-ventral axis formation;  04340 :Hedgehog signaling pathway;  04350 :TGF-beta signaling pathway;  04360 :Axon guidance;  04370 :VEGF signaling pathway;  04510 :Focal adhesion;  04520 :Adherens junction;  04530 :Tight junction;  04540 :Gap junction;  04620 :Toll-like receptor signaling pathway;  04630 :Jak-STAT signaling pathway;  04660 :T cell receptor signaling pathway;  04662 :B cell receptor signaling pathway;  04664 :Fc epsilon RI signaling pathway;  04720 :Long-term potentiation;  04730 :Long-term depression;  04810 :Regulation of actin cytoskeleton;  04910 :Insulin signaling pathway;  04912 :GnRH signaling pathway;  04920 :Adipocytokine signaling pathway;  05010 :Alzheimer's disease;  05210 :Colorectal cancer; 
Protein-protein interaction (PPI) PPI viewer H-Inv protein ID HIP000012434
No. of interaction 5
Interaction partner(s) HIP000034909HIP000058989HIP000070686HIP000089951HIP000093088
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl NA
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:27-May-2015
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:27-May-2015
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

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
35 ^ 36 -/G rs199957738 + 5'UTR
238 .. 238 T/C rs146920577 + 5'UTR
254 .. 254 A/C rs138017154 + 5'UTR
318 .. 318 C/T rs143943580 + 5'UTR
334 .. 334 T/G rs148671562 + 5'UTR
542 .. 542 A/G rs141256626 + CDS Synonymous[Thr64Thr]
563 .. 563 C/T rs11546478 + CDS Synonymous[Phe71Phe]
572 .. 572 C/T rs150808056 + CDS Synonymous[Tyr74Tyr]
749 .. 749 C/T rs137978439 + CDS Synonymous[Tyr133Tyr]
782 .. 782 C/T rs149513190 + CDS Synonymous[His144His]
875 .. 875 T/A rs144007479 + CDS Synonymous[Pro175Pro]
885 .. 885 T/A rs148276213 + CDS Nonsynonymous[Ser179Thr]
893 .. 893 C/T rs141884969 + CDS Synonymous[His181His]
962 .. 962 C/T rs141959001 + CDS Synonymous[Tyr204Tyr]
1007 .. 1007 C/T rs144664066 + CDS Synonymous[Phe219Phe]
1073 .. 1073 G/A rs140970872 + CDS Synonymous[Thr241Thr]
1121 .. 1121 C/T rs139144760 + CDS Synonymous[His257His]
1235 .. 1235 C/G rs140924363 + CDS Synonymous[Ala295Ala]
1309 .. 1309 G/A rs150231592 + CDS Nonsynonymous[Arg320His]
1316 .. 1316 T/G rs36170987 + CDS Synonymous[Val322Val]
1329 .. 1329 C/T rs62644536 + CDS Nonsynonymous[Arg327Trp]
1334 .. 1334 C/T rs11546480 + CDS Synonymous[Asp328Asp]
1338 .. 1338 G/A rs145750007 + CDS Nonsynonymous[Val330Met]
1347 .. 1347 G/A rs36139924 + CDS Nonsynonymous[Asp333Asn]
1406 .. 1406 G/A rs143027699 + CDS Synonymous[Ala352Ala]
1442 .. 1442 A/G rs36173075 + 3'UTR
1453 .. 1453 G/C rs36138803 + 3'UTR
1457 .. 1457 G/A rs141144359 + 3'UTR
1479 .. 1479 G/A rs190305972 + 3'UTR
1482 .. 1482 C/T rs11546477 + 3'UTR
1502 .. 1502 C/T rs150747032 + 3'UTR
1529 .. 1529 C/T rs139509186 + 3'UTR
1530 .. 1530 G/A rs143650974 + 3'UTR
1618 .. 1618 G/A rs147183623 + 3'UTR
1625 .. 1625 G/A rs182516015 + 3'UTR
1643 .. 1643 G/A rs140489559 + 3'UTR
1647 .. 1647 G/A rs11546481 + 3'UTR
1649 .. 1649 C/T rs185910187 + 3'UTR
1650 .. 1650 G/A rs144606574 + 3'UTR
1653 .. 1653 G/A rs148728305 + 3'UTR
1710 .. 1710 T/C rs142252355 + 3'UTR
1739 .. 1739 C/T rs191201474 + 3'UTR
1888 .. 1888 C/T rs182205590 + 3'UTR
1945 .. 1945 G/A rs151275643 + 3'UTR
1958 .. 1958 G/A rs140588788 + 3'UTR
1968 .. 1968 G/A rs144420589 + 3'UTR
1977 .. 1977 C/T rs185304057 + 3'UTR
1978 .. 1978 G/A rs11546479 + 3'UTR
1979 .. 1979 C/T rs1134015 + 3'UTR
2044 .. 2044 C/T rs150281021 + 3'UTR
2165 .. 2165 T/C rs138921693 + 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