H-InvDB_9.0 released on May 27, 2015.
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H-Inv ID (HIT)
H-Inv cluster ID (HIX)
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Definition*
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---
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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;
Select format
Flat file
XML file
Nucleotide sequence fasta
Protein sequence fasta
Transcript original information
Accession number
BC011752.2
CAGE tag ID
NA
EST ID
NA
Clone Number
MGC:19710 IMAGE:3534047
Experimental resources
NBRC
;
HGPD
;
Antibody (MBD4)
;
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
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
GCGTTGCGGCGCTGGGCTCGTTGCTGCAGCCGGACCCTGCTCGATGGGCA CGACTGGGCTGGAGAGTCTGAGTCTGGGGGACCGCGGAGCTGCCCCCACC GTCACCTCTAGTGAGCGCCTAGTCCCAGACCCGCCGAATGACCTCCGCAA AGAAGATGTTGCTATGGAATTGGAAAGAGTGGGAGAAGATGAGGAACAAA TGATGATAAAAAGAAGCAGTGAATGTAATCCCTTGCTACAAGAACCCATC GCTTCTGCTCAGTTTGGTGCTACTGCAGGAACAGAATGCCGTAAGTCTGT CCCATGTGGATGGGAAAGAGTTGTGAAGCAAAGGTTATTTGGGAAGACAG CAGGAAGATTTGATGTGTACTTTATCAGCCCACAAGGACTGAAGTTCAGA TCCAAAAGTTCACTTGCTAATTATCTTCACAAAAATGGAGAGACTTCTCT TAAGCCAGAAGATTTTGATTTTACTGTACTTTCTAAAAGGGGTATCAAGT CAAGATATAAAGACTGCAGCATGGCAGCCCTGACATCCCATCTACAAAAC CAAAGTAACAATTCAAACTGGAACCTCAGGACCCGAAGCAAGTGCAAAAA GGATGTGTTTATGCCGCCAAGTAGTAGTTCAGAGTTGCAGGAGAGCAGAG GACTCTCTAACTTTACTTCCACTCATTTGCTTTTGAAAGAAGATGAGGGT GTTGATGATGTTAACTTCAGAAAGGTTAGAAAGCCCAAAGGAAAGGTGAC TATTTTGAAAGGAATCCCAATTAAGAAAACTAAAAAAGGATGTAGGAAGA GCTGTTCAGGTTTTGTTCAAAGTGATAGCAAAAGAGAATCTGTGTGTAAT AAAGCAGATGCTGAAAGTGAACCTGTTGCACAAAAAAGTCAGCTTGATAG AACTGTCTGCATTTCTGATGCTGGAGCATGTGGTGAGACCCTCAGTGTGA CCAGTGAAGAAAACAGCCTTGTAAAAAAAAAAGAAAGATCATTGAGTTCA GGATCAAATTTTTGTTCTGAACAAAAAACTTCTGGCATCATAAACAAATT TTGTTCAGCCAAAGACTCAGAACACAACGAGAAGTATGAGGATACCTTTT TAGAATCTGAAGAAATCGGAACAAAAGTAGAAGTTGTGGAAAGGAAAGAA CATTTGCATACTGACATTTTAAAACGTGGCTCTGAAATGGACAACAACTG CTCACCAACCAGGAAAGACTTCACTGAAGATACCATCCCACGAACACAGA TAGAAAGAAGGAAAACAAGCCTGTATTTTTCCAGCAAATATAACAAAGAA GCTCTTAGCCCCCCACGACGTAAAGCCTTTAAGAAATGGACACCTCCTCG GTCACCTTTTAATCTCGTTCAAGAAACACTTTTTCATGATCCATGGAAGC TTCTCATCGCTACTATATTTCTCAATCGGACCTCAGGCAAAATGGCAATA CCTGTGCTTTGGAAGTTTCTGGAGAAGTATCCTTCAGCTGAGGTAGCAAG AACCGCAGACTGGAGAGATGTGTCAGAACTTCTTAAACCTCTTGGTCTCT ACGATCTTCGGGCAAAAACCATTGTCAAGTTCTCAGATGAATACCTGACA AAGCAGTGGAAGTATCCAATTGAGCTTCATGGGATTGGTAAATATGGCAA CGACTCTTACCGAATTTTTTGTGTCAATGAGTGGAAGCAGGTGCACCCTG AAGACCACAAATTAAATAAATATCATGACTGGCTTTGGGAAAATCATGAA AAATTAAGTCTATCTTAAACTCTGCAGCTTTCAAGCTCATCTGTTATGCA TAGCTTTGCACTTCAAAAAAGCTTAATTAAGTACAACCAACCACCTTTCC AGCCATAGAGATTTTAATTAGCCCAACTAGAAGCCTAGTGTGTGTGCTTT CTTAATGTGTGTGCCAATGGTGGATCTTTGCTACTGAATGTGTTTGAACA TGTTTTGAGATTTTTTTAAAATAAATTATTATTTGACAACAAAAAAAAAA AAAAAAAAAAAA
Gene structure information
H-Inv cluster ID
HIX0003669
Genomic location
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
MBD4
;
*GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links
H-DBAS
;
G-integra
;
cDNA-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
;
MGTTGLESLSLGDRGAAPTVTSSERLVPDPPNDLRKEDVAMELERVGEDE EQMMIKRSSECNPLLQEPIASAQFGATAGTECRKSVPCGWERVVKQRLFG KTAGRFDVYFISPQGLKFRSKSSLANYLHKNGETSLKPEDFDFTVLSKRG IKSRYKDCSMAALTSHLQNQSNNSNWNLRTRSKCKKDVFMPPSSSSELQE SRGLSNFTSTHLLLKEDEGVDDVNFRKVRKPKGKVTILKGIPIKKTKKGC RKSCSGFVQSDSKRESVCNKADAESEPVAQKSQLDRTVCISDAGACGETL SVTSEENSLVKKKERSLSSGSNFCSEQKTSGIINKFCSAKDSEHNEKYED TFLESEEIGTKVEVVERKEHLHTDILKRGSEMDNNCSPTRKDFTEDTIPR TQIERRKTSLYFSSKYNKEALSPPRRKAFKKWTPPRSPFNLVQETLFHDP WKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPL GLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQV HPEDHKLNKYHDWLWENHEKLSLS*
Motif information
a.a.
length
InterPro
Name
125
IPR001739
Methyl-CpG DNA binding [Domain]
121
IPR016177
DNA-binding domain [Domain]
73
IPR001739
Methyl-CpG DNA binding [Domain]
77
IPR001739
Methyl-CpG DNA binding [Domain]
70
IPR001739
Methyl-CpG DNA binding [Domain]
146
IPR011257
DNA glycosylase [Domain]
138
IPR011257
DNA glycosylase [Domain]
75
IPR003265
HhH-GPD domain [Domain]
Gene function information
H-Inv ID
HIT000035425
H-Inv cluster ID
HIX0003669
Accession number
BC011752.2
CAGE tag ID
NA
EST ID
NA
Transcript feature
NO;
Coding potential
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
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
9774669
;
10097147
;
10441743
;
10930409
;
12702765
;
15489334
;
18669648
;
ALL
;
Gene family/group
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)
H-Inv protein ID
HIP000061507
No. of interaction
27
Interaction partner(s)
HIP000023532
;
HIP000023532
;
HIP000027524
;
HIP000032269
;
HIP000036836
;
HIP000045818
;
HIP000050187
;
HIP000059982
;
HIP000059982
;
HIP000064883
;
HIP000066953
;
HIP000082533
;
HIP000084384
;
HIP000096381
;
HIP000100152
;
HIP000100152
;
HIP000106486
;
HIP000109916
;
HIP000110238
;
HIP000112664
;
HIP000112664
;
HIP000117036
;
HIP000117036
;
HIP000136553
;
HIP000136553
;
HIP000258575
;
HIP000259487
;
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
MBD4
;
*GeneCards is provided free to academic non-profit institutions.
etc
Human-Gene diversity Of Life-style related Diseases
;
Curation status
Auto-annotated
Notes
NA
Related H-InvDB links
Gene family;
Similarity Search Tool;
TACT
;
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;
JRE-1.4.0 or later is required.
Download JRE at
Sun's web site.
Protein structure information (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
Gene expression information
Last modified:27-May-2015
Tissue-specific expression
NA
Probe
information
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-ANGEL
;
DNAProbeLocator
;
Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information
Single Nucleotide Polymorphism (SNP) and indel
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
No data available
Database links
Human-Gene diversity Of Life-style related Diseases(H-GOLD)
;
Related H-InvDB links
VaryGene
;
Repeat Mask Viewer
;