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: HIT000035425 Accession number: BC011752 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Methyl-CpG-binding domain protein 4; EC=3.2.2.-; Methyl-CpG-binding endonuclease 1; Methyl-CpG-binding protein MBD4; Mismatch-specific DNA N-glycosylase;
 
 

Transcript original information
Accession number BC011752.2
CAGE tag ID NA
EST ID NA
Clone Number MGC:19710 IMAGE:3534047
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (MBD4) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (MBD4);
Sequence data provider Provider:MGC/NCI
Annotation project H-Invitational FLcDNA
Length of cDNA 2012[bp] (No. of exon:8)[A:673 T:511 G:440 C:388]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Lung, small cell carcinoma
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 1991(+) Signal: 1970-1974(+)
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) CAGAAG; 
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0003669
Genomic location  G-integra Help Chromosome 3
Location 3q21.3
Position 129150121- 129158719
Strand -
Possible duplicated location(s) NA
Gene structure 8 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:8930
KEGG GENES KEGG GENES(8930)
GeneCard GeneCardMBD4*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 HIP000061507
Predicted CDS 44..1768;  574[aa];  Orientation:+2; 
Codon Adaptation Index (CAI). 0.725
Database links RefSeq NP_001263199
UniProt NA
CCDS CCDS63768

Motif information
ORF

length(574),orf(44:1768)
MGTTGLESLSLGDRGAAPTVTSSERLVPDPPNDLRKEDVAMELERVGEDE
EQMMIKRSSECNPLLQEPIASAQFGATAGTECRKSVPCGWERVVKQRLFG
KTAGRFDVYFISPQGLKFRSKSSLANYLHKNGETSLKPEDFDFTVLSKRG
IKSRYKDCSMAALTSHLQNQSNNSNWNLRTRSKCKKDVFMPPSSSSELQE
SRGLSNFTSTHLLLKEDEGVDDVNFRKVRKPKGKVTILKGIPIKKTKKGC
RKSCSGFVQSDSKRESVCNKADAESEPVAQKSQLDRTVCISDAGACGETL
SVTSEENSLVKKKERSLSSGSNFCSEQKTSGIINKFCSAKDSEHNEKYED
TFLESEEIGTKVEVVERKEHLHTDILKRGSEMDNNCSPTRKDFTEDTIPR
TQIERRKTSLYFSSKYNKEALSPPRRKAFKKWTPPRSPFNLVQETLFHDP
WKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPL
GLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQV
HPEDHKLNKYHDWLWENHEKLSLS*
a.a.
length
InterPro Name
length(125), motif(57:181) 125 IPR001739 Methyl-CpG DNA binding [Domain]
length(121), motif(60:180) 121 IPR016177 DNA-binding domain [Domain]
length(73), motif(76:148) 73 IPR001739 Methyl-CpG DNA binding [Domain]
length(77), motif(79:155) 77 IPR001739 Methyl-CpG DNA binding [Domain]
length(70), motif(80:149) 70 IPR001739 Methyl-CpG DNA binding [Domain]
length(146), motif(424:569) 146 IPR011257 DNA glycosylase [Domain]
length(138), motif(433:570) 138 IPR011257 DNA glycosylase [Domain]
length(75), motif(455:529) 75 IPR003265 HhH-GPD domain [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000035425
H-Inv cluster ID Locus viewHIX0003669
Accession number BC011752.2
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Methyl-CpG-binding domain protein 4; EC=3.2.2.-; Methyl-CpG-binding endonuclease 1; Methyl-CpG-binding protein MBD4; Mismatch-specific DNA N-glycosylase;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (O95243)  [Identity/coverage = 98.966%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 9774669100971471044174310930409127027651548933418669648ALL
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 MBD4
HGNC aliases NA
HGNC name methyl-CpG binding domain protein 4
DDBJ MBD4
UniProt MBD4
EC number EC 3.2.2.-Hydrolysing N-Glycosyl Compounds; 
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 HIP000061507
No. of interaction 27
Interaction partner(s) HIP000023532HIP000023532HIP000027524HIP000032269HIP000036836HIP000045818HIP000050187HIP000059982HIP000059982HIP000064883HIP000066953HIP000082533HIP000084384HIP000096381HIP000100152HIP000100152HIP000106486HIP000109916HIP000110238HIP000112664HIP000112664HIP000117036HIP000117036HIP000136553HIP000136553HIP000258575HIP000259487
BIND 12795;  130753; 
DIP NA
MINT MINT-45869;  MINT-45870;  MINT-62615;  MINT-62713;  MINT-62789; 
HPRD 00278;  00390;  03909; 
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:8930
KEGG GENES KEGG GENES(8930)
GeneCard GeneCardMBD4*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. 
NA

Gene ontology information
Molecular function catalytic activity (GO:0003824);  DNA binding (GO:0003677); 
Biological process DNA repair (GO:0006281);  base-excision repair (GO:0006284); 
Cellular component nucleus (GO:0005634); 

Subcellular localization information  Last modified:27-May-2015
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:27-May-2015
Start End PDB_ID E-value Identity Coverage SCOP_ID
86 156 1ub1A 7e-19 50.7 71/125 d.10.1.3
431 574 1ngnA 6e-29 96.5 144/144 a.96.1.2
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:27-May-2015
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator
AceGene AGhsA221403; 
Affymetrix
GeneChip
HG-Focus 214047_s_at; 
HG-U133 209579_s_at;  209580_s_at;  214047_s_at; 
HG-U133A 209579_s_at;  209580_s_at;  214047_s_at; 
HG-U133A_2 209579_s_at;  209580_s_at;  214047_s_at; 
HG-U133B NA
HG-U133_Plus_2 209579_s_at;  209580_s_at;  214047_s_at; 
HG-U95 34386_at; 
HG-U95A 34386_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2641666;  2694787;  2694788;  2694789;  2694793;  2694794;  2694796;  2694798;  2694800;  2694801;  2694802;  2694803;  2694804;  2694805;  2694806;  2694807;  2694808; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 A_23_P92154; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P92154; 
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
53 .. 53 A/G rs150778761 - CDS Nonsynonymous[Thr4Ala]
65 .. 65 A/G rs143075296 - CDS Nonsynonymous[Ser8Gly]
74 .. 74 C/T rs2307297 + CDS Synonymous[Leu11Leu]
154 .. 154 A/T rs200224645 - CDS Nonsynonymous[Glu37Asp]
179 .. 179 G/A rs200883484 - CDS Nonsynonymous[Val46Met]
182 .. 182 G/A rs147232960 - CDS Nonsynonymous[Gly47Arg]
224 .. 224 T/C rs2307296 + CDS Nonsynonymous[Cys61Arg]
260 .. 260 C/G rs148098584 - CDS Nonsynonymous[Gln73Glu]
272 .. 272 A/G rs143811380 - CDS Nonsynonymous[Thr77Ala]
362 .. 362 G/T rs201697944 - CDS Nonsynonymous[Asp107Tyr]
379 .. 379 C/T rs61753468 - CDS Synonymous[Ser112Ser]
390 .. 390 T/G rs200082149 - CDS Nonsynonymous[Leu116Arg]
407 ^ 408 -/A rs34275677 - CDS
411 .. 411 C/T rs201341528 - CDS Nonsynonymous[Ser123Leu]
446 .. 446 T/G rs200851180 - CDS Nonsynonymous[Ser135Ala]
458 .. 458 G/C rs186316895 - CDS Nonsynonymous[Glu139Gln]
478 .. 478 A/G rs199785676 - CDS Synonymous[Val145Val]
508 .. 508 T/C rs138876144 - CDS Synonymous[Tyr155Tyr]
526 .. 526 A/T rs142605003 - CDS Synonymous[Ala161Ala]
558 .. 558 A/G rs145116757 - CDS Nonsynonymous[Asn172Ser]
585 .. 585 G/A rs180996357 - CDS Nonsynonymous[Arg181Gln]
611 .. 611 A/T rs140265312 - CDS Nonsynonymous[Met190Leu]
615 .. 615 C/T rs148464573 - CDS Nonsynonymous[Pro191Leu]
616 .. 616 G/A rs201684514 - CDS Synonymous[Pro191Pro]
694 .. 694 T/C rs201331346 - CDS Synonymous[Asp217Asp]
710 .. 710 G/A rs143317948 - CDS Nonsynonymous[Val223Ile]
723 .. 723 A/G rs199828331 - CDS Nonsynonymous[Lys227Arg]
725 .. 725 G/C rs140696334 - CDS Nonsynonymous[Val228Leu]
726 .. 726 T/A rs150940003 - CDS Nonsynonymous[Val228Asp]
745 .. 745 G/A rs78797976 - CDS Synonymous[Lys234Lys]
750 .. 750 C/T rs142668030 - CDS Nonsynonymous[Thr236Ile]
755 .. 755 T/C rs79326124 - CDS Synonymous[Leu238Leu]
860 .. 860 G/A/T rs10342 + CDS
882 .. 882 A/T rs200642994 - CDS Nonsynonymous[Gln280Leu]
883 .. 883 A/G rs147394477 - CDS Synonymous[Gln280Gln]
1067 .. 1067 T/C rs2307289 + CDS Nonsynonymous[Ser342Pro]
1079 .. 1079 G/A rs140693 + CDS Nonsynonymous[Glu346Lys]
1115 .. 1115 A/T rs147270686 - CDS Nonsynonymous[Ile358Phe]
1116 .. 1116 T/C rs2307298 + CDS Nonsynonymous[Ile358Thr]
1117 .. 1117 C/T rs139242730 - CDS Synonymous[Ile358Ile]
1151 .. 1151 C/T rs150831027 - CDS Nonsynonymous[His370Tyr]
1175 .. 1175 C/T rs149311534 - CDS Nonsynonymous[Arg378Cys]
1202 .. 1202 T/G rs141556272 - CDS Nonsynonymous[Ser387Ala]
1203 .. 1203 C/T rs200169155 - CDS Nonsynonymous[Ser387Leu]
1220 .. 1220 T/A rs188172372 - CDS Nonsynonymous[Phe393Ile]
1249 .. 1249 G/A rs3138351 + CDS Synonymous[Gln402Gln]
1262 .. 1262 A/G rs200315861 - CDS Nonsynonymous[Lys407Glu]
1264 .. 1264 A/G rs201351149 - CDS Synonymous[Lys407Lys]
1265 .. 1265 A/G rs202188508 - CDS Nonsynonymous[Thr408Ala]
1287 .. 1287 A/G rs147756381 - CDS Nonsynonymous[Lys415Arg]
1311 .. 1311 C/T rs148378664 - CDS Nonsynonymous[Pro423Leu]
1320 .. 1320 G/A rs200137916 - CDS Nonsynonymous[Arg426His]
1350 .. 1350 G/A rs200995882 - CDS Nonsynonymous[Arg436Gln]
1408 .. 1408 C/T rs201776693 - CDS Synonymous[Ile455Ile]
1425 .. 1425 A/G rs78782061 - CDS Nonsynonymous[Asn461Ser]
1438 .. 1438 C/T rs140696 + CDS Synonymous[Gly465Gly]
1578 .. 1578 A/G rs138445306 - CDS Nonsynonymous[Lys512Arg]
1597 .. 1597 G/A rs144657741 - CDS Synonymous[Leu518Leu]
1619 .. 1619 A/G rs183820888 - CDS Nonsynonymous[Ile526Val]
1623 .. 1623 A/T rs191518400 - CDS Nonsynonymous[Glu527Val]
1633 .. 1633 G/A rs2005619 + CDS Synonymous[Gly530Gly]
1638 .. 1638 G/A rs202021161 - CDS Nonsynonymous[Gly532Asp]
1702 .. 1702 A/G rs2307286 + CDS Synonymous[Glu553Glu]
1713 .. 1713 T/A rs200758755 - CDS AA-STOP[Leu557*]
1727 .. 1727 G/C rs2307293 + CDS Nonsynonymous[Asp562His]
1804 .. 1804 C/T rs180861060 - 3'UTR
1888 .. 1888 G/A rs190790404 - 3'UTR
1968 .. 1968 A/T rs185483849 - 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