GGRNA Home | Help | Advanced search

2024-03-29 20:50:52, GGRNA : RefSeq release 60 (20130726)

LOCUS       NM_001276271            2338 bp    mRNA    linear   PRI 14-MAY-2013
DEFINITION  Homo sapiens methyl-CpG binding domain protein 4 (MBD4), transcript
            variant 3, mRNA.
ACCESSION   NM_001276271
VERSION     NM_001276271.1  GI:442796451
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2338)
  AUTHORS   Otani,J., Arita,K., Kato,T., Kinoshita,M., Kimura,H., Suetake,I.,
            Tajima,S., Ariyoshi,M. and Shirakawa,M.
  TITLE     Structural basis of the versatile DNA recognition ability of the
            methyl-CpG binding domain of methyl-CpG binding domain protein 4
  JOURNAL   J. Biol. Chem. 288 (9), 6351-6362 (2013)
   PUBMED   23316048
  REMARK    GeneRIF: the crystal structure of MBD4 bound to
            5-hydroxymethylcytosine further demonstrates that MBDMBD4 is able
            to recognize a wide range of 5-methylcytosine modifications
REFERENCE   2  (bases 1 to 2338)
  AUTHORS   Xiong,X.D., Luo,X.P., Liu,X., Jing,X., Zeng,L.Q., Lei,M., Hong,X.S.
            and Chen,Y.
  TITLE     The MBD4 Glu346Lys polymorphism is associated with the risk of
            cervical cancer in a Chinese population
  JOURNAL   Int. J. Gynecol. Cancer 22 (9), 1552-1556 (2012)
   PUBMED   23027038
  REMARK    GeneRIF: MBD4 Glu346Lys polymorphism is associated with the risk of
            cervical cancer in a Chinese population.
REFERENCE   3  (bases 1 to 2338)
  AUTHORS   Morera,S., Grin,I., Vigouroux,A., Couve,S., Henriot,V.,
            Saparbaev,M. and Ishchenko,A.A.
  TITLE     Biochemical and structural characterization of the glycosylase
            domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing
            DNA
  JOURNAL   Nucleic Acids Res. 40 (19), 9917-9926 (2012)
   PUBMED   22848106
  REMARK    GeneRIF: Crystal structures of human MBD4(catalytic domain) reveal
            that MBD4 uses a base flipping mechanism to specifically recognize
            thymine and 5-hydroxymethyluracil.
REFERENCE   4  (bases 1 to 2338)
  AUTHORS   Manvilla,B.A., Maiti,A., Begley,M.C., Toth,E.A. and Drohat,A.C.
  TITLE     Crystal structure of human methyl-binding domain IV glycosylase
            bound to abasic DNA
  JOURNAL   J. Mol. Biol. 420 (3), 164-175 (2012)
   PUBMED   22560993
  REMARK    GeneRIF: specificity of MBD4 for acting at CpG sites depends
            largely on its methyl-CpG-binding domain, which binds preferably to
            G.T mispairs in a methylated CpG site
REFERENCE   5  (bases 1 to 2338)
  AUTHORS   Lin,Y. and Li,W.
  TITLE     MBD 4--a potential substrate for protein kinase X
  JOURNAL   Acta Biochim. Biophys. Sin. (Shanghai) 43 (11), 916-917 (2011)
   PUBMED   21971312
  REMARK    GeneRIF: MBD 4--a potential substrate for protein kinase X
REFERENCE   6  (bases 1 to 2338)
  AUTHORS   Hendrich,B., Hardeland,U., Ng,H.H., Jiricny,J. and Bird,A.
  TITLE     The thymine glycosylase MBD4 can bind to the product of deamination
            at methylated CpG sites
  JOURNAL   Nature 401 (6750), 301-304 (1999)
   PUBMED   10499592
  REMARK    Erratum:[Nature 2000 Mar 30;404(6777):525]
REFERENCE   7  (bases 1 to 2338)
  AUTHORS   Hendrich,B., Abbott,C., McQueen,H., Chambers,D., Cross,S. and
            Bird,A.
  TITLE     Genomic structure and chromosomal mapping of the murine and human
            Mbd1, Mbd2, Mbd3, and Mbd4 genes
  JOURNAL   Mamm. Genome 10 (9), 906-912 (1999)
   PUBMED   10441743
REFERENCE   8  (bases 1 to 2338)
  AUTHORS   Bellacosa,A., Cicchillitti,L., Schepis,F., Riccio,A., Yeung,A.T.,
            Matsumoto,Y., Golemis,E.A., Genuardi,M. and Neri,G.
  TITLE     MED1, a novel human methyl-CpG-binding endonuclease, interacts with
            DNA mismatch repair protein MLH1
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 96 (7), 3969-3974 (1999)
   PUBMED   10097147
REFERENCE   9  (bases 1 to 2338)
  AUTHORS   Boland,C.R., Thibodeau,S.N., Hamilton,S.R., Sidransky,D.,
            Eshleman,J.R., Burt,R.W., Meltzer,S.J., Rodriguez-Bigas,M.A.,
            Fodde,R., Ranzani,G.N. and Srivastava,S.
  TITLE     A National Cancer Institute Workshop on Microsatellite Instability
            for cancer detection and familial predisposition: development of
            international criteria for the determination of microsatellite
            instability in colorectal cancer
  JOURNAL   Cancer Res. 58 (22), 5248-5257 (1998)
   PUBMED   9823339
  REMARK    Review article
REFERENCE   10 (bases 1 to 2338)
  AUTHORS   Hendrich,B. and Bird,A.
  TITLE     Identification and characterization of a family of mammalian
            methyl-CpG binding proteins
  JOURNAL   Mol. Cell. Biol. 18 (11), 6538-6547 (1998)
   PUBMED   9774669
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL449212.1.
            
            Summary: The protein encoded by this gene is a member of a family
            of nuclear proteins related by the presence of a methyl-CpG binding
            domain (MBD). These proteins are capable of binding specifically to
            methylated DNA, and some members can also repress transcription
            from methylated gene promoters. This protein contains an MBD domain
            at the N-terminus that functions both in binding to methylated DNA
            and in protein interactions and a C-terminal mismatch-specific
            glycosylase domain that is involved in DNA repair. Alternatively
            spliced transcript variants encoding multiple isoforms have been
            observed for this gene. [provided by RefSeq, Jan 2013].
            
            Transcript Variant: This variant (3) lacks an exon and its
            transcription extends past a splice site that is used in variant 1,
            resulting in a novel 3' coding region and 3' UTR compared to
            variant 1. It encodes isoform 3 which is shorter and has a distinct
            C-terminus, compared to isoform 1.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK303013.1 [ECO:0000332]
            RNAseq introns              :: mixed/partial sample support
                                           ERS025081, ERS025082 [ECO:0000350]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-450               AL449212.1         59758-60207         c
            451-681             AL449212.1         57748-57978         c
            682-1547            AL449212.1         56471-57336         c
            1548-1622           AL449212.1         54090-54164         c
            1623-1757           AL449212.1         53878-54012         c
            1758-1907           AL449212.1         53126-53275         c
            1908-2338           AL449212.1         52204-52634         c
FEATURES             Location/Qualifiers
     source          1..2338
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3q21.3"
     gene            1..2338
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /note="methyl-CpG binding domain protein 4"
                     /db_xref="GeneID:8930"
                     /db_xref="HGNC:6919"
                     /db_xref="MIM:603574"
     exon            1..450
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /inference="alignment:Splign:1.39.8"
     variation       55
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:3138334"
     variation       232
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="a"
                     /replace="t"
                     /db_xref="dbSNP:2307292"
     misc_feature    266..268
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /note="upstream in-frame stop codon"
     CDS             347..2065
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /note="isoform 3 is encoded by transcript variant 3;
                     3,N(4)-ethenocytosine glycosylase; G/T mismatch
                     glycosylase; G/U mismatch glycosylase; G/5-fluorouracil
                     mismatch glycosylase with biphasic kinetics; putative
                     methyl-CpG binding protein; methyl-CpG-binding protein
                     MBD4; methyl-CpG-binding endonuclease 1; mismatch-specific
                     DNA N-glycosylase"
                     /codon_start=1
                     /product="methyl-CpG-binding domain protein 4 isoform 3"
                     /protein_id="NP_001263200.1"
                     /db_xref="GI:442796452"
                     /db_xref="GeneID:8930"
                     /db_xref="HGNC:6919"
                     /db_xref="MIM:603574"
                     /translation="
MGTTGLESLSLGDRGAAPTVTSSERLVPDPPNDLRKEDVAMELERVGEDEEQMMIKRSSECNPLLQEPIASAQFGATAGTECRKSVPCGWERVVKQRLFGKTAGRFDVYFISPQGLKFRSKSSLANYLHKNGETSLKPEDFDFTVLSKRGIKSRYKDCSMAALTSHLQNQSNNSNWNLRTRSKCKKDVFMPPSSSSELQESRGLSNFTSTHLLLKEDEGVDDVNFRKVRKPKGKVTILKGIPIKKTKKGCRKSCSGFVQSDSKRESVCNKADAESEPVAQKSQLDRTVCISDAGACGETLSVTSEENSLVKKKERSLSSGSNFCSEQKTSGIINKFCSAKDSEHNEKYEDTFLESEEIGTKVEVVERKEHLHTDILKRGSEMDNNCSPTRKDFTGEKIFQEDTIPRTQIERRKTSLYFSSKYNKEALSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVRLTPIHNSAHLVSEAK
"
     misc_feature    581..811
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /note="Methyl-CpG binding domain; Region: MBD; smart00391"
                     /db_xref="CDD:128673"
     misc_feature    order(623..625,629..631,635..637,659..661,665..667,
                     692..694,701..703,713..715)
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:29025"
     misc_feature    1727..>2005
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /note="endonuclease III; includes endonuclease III
                     (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA
                     glycosidases (Alka-family) and other DNA glycosidases;
                     Region: ENDO3c; cl14786"
                     /db_xref="CDD:209897"
     misc_feature    order(1748..1756,1763..1765,1880..1882)
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /note="minor groove reading motif; other site"
                     /db_xref="CDD:28938"
     misc_feature    1946..1966
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /note="helix-hairpin-helix signature motif; other site"
                     /db_xref="CDD:28938"
     variation       377
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:2307297"
     exon            451..681
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /inference="alignment:Splign:1.39.8"
     variation       527
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:2307296"
     exon            682..1547
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /inference="alignment:Splign:1.39.8"
     variation       1163
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="a"
                     /replace="g"
                     /replace="t"
                     /db_xref="dbSNP:10342"
     variation       1370
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:2307289"
     variation       1382
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:140693"
     variation       1419
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:2307298"
     exon            1548..1622
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /inference="alignment:Splign:1.39.8"
     variation       1570
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:3138351"
     exon            1623..1757
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /inference="alignment:Splign:1.39.8"
     exon            1758..1907
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /inference="alignment:Splign:1.39.8"
     variation       1759
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:140696"
     exon            1908..2338
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /inference="alignment:Splign:1.39.8"
     variation       1954
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:2005619"
     variation       2172
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="c"
                     /replace="t"
                     /db_xref="dbSNP:2005620"
     variation       2187
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:3138360"
     variation       2219
                     /gene="MBD4"
                     /gene_synonym="MED1"
                     /replace="a"
                     /replace="g"
                     /db_xref="dbSNP:3138361"
ORIGIN      
cttgctccgagcgcgcatgtccgaaagggaaagccagaaaagcagcaaaagcaatggtggcactggagcccctaaggcgccagcgcaaccagagcgcgagcgattggtcggggcgtgtgggggcggtgcgtcttcctcgagaatggatttgattggtggagcgtggaaatggcggctgtagccgagggggcggccggaaagcagcggcggcgtctggggcgctttcgcaacattcagacctcggttgcagcccggtgccgtgagctgaagaggtttcacatcttactccgccccacaccctgggcgttgcggcgctgggctcgttgctgcagccggaccctgctcgatgggcacgactgggctggagagtctgagtctgggggaccgcggagctgcccccaccgtcacctctagtgagcgcctagtcccagacccgccgaatgacctccgcaaagaagatgttgctatggaattggaaagagtgggagaagatgaggaacaaatgatgataaaaagaagcagtgaatgtaatcccttgctacaagaacccatcgcttctgctcagtttggtgctactgcaggaacagaatgccgtaagtctgtcccatgtggatgggaaagagttgtgaagcaaaggttatttgggaagacagcaggaagatttgatgtgtactttatcagcccacaaggactgaagttcagatccaaaagttcacttgctaattatcttcacaaaaatggagagacttctcttaagccagaagattttgattttactgtactttctaaaaggggtatcaagtcaagatataaagactgcagcatggcagccctgacatcccatctacaaaaccaaagtaacaattcaaactggaacctcaggacccgaagcaagtgcaaaaaggatgtgtttatgccgccaagtagtagttcagagttgcaggagagcagaggactctctaactttacttccactcatttgcttttgaaagaagatgagggtgttgatgatgttaacttcagaaaggttagaaagcccaaaggaaaggtgactattttgaaaggaatcccaattaagaaaactaaaaaaggatgtaggaagagctgttcaggttttgttcaaagtgatagcaaaagagaatctgtgtgtaataaagcagatgctgaaagtgaacctgttgcacaaaaaagtcagcttgatagaactgtctgcatttctgatgctggagcatgtggtgagaccctcagtgtgaccagtgaagaaaacagccttgtaaaaaaaaaagaaagatcattgagttcaggatcaaatttttgttctgaacaaaaaacttctggcatcataaacaaattttgttcagccaaagactcagaacacaacgagaagtatgaggatacctttttagaatctgaagaaatcggaacaaaagtagaagttgtggaaaggaaagaacatttgcatactgacattttaaaacgtggctctgaaatggacaacaactgctcaccaaccaggaaagacttcactggtgagaaaatatttcaagaagataccatcccacgaacacagatagaaagaaggaaaacaagcctgtatttttccagcaaatataacaaagaagctcttagccccccacgacgtaaagcctttaagaaatggacacctcctcggtcaccttttaatctcgttcaagaaacactttttcatgatccatggaagcttctcatcgctactatatttctcaatcggacctcaggcaaaatggcaatacctgtgctttggaagtttctggagaagtatccttcagctgaggtagcaagaaccgcagactggagagatgtgtcagaacttcttaaacctcttggtctctacgatcttcgggcaaaaaccattgtcaagttctcagatgaatacctgacaaagcagtggaagtatccaattgagcttcatgggattggtaaatatggcaacgactcttaccgaattttttgtgtcaatgagtggaagcaggtgaggctcactcccatccataattcagcacatttggtctctgaggcaaaataagtccaccattatggttaagactatttattggatacaaatgctattacagtcacaaacaattgtgttcctggctgcggggaagcgggtggcatgtgggttttggggtttttgatcagtaggcgctcccaagtccacaaagaccagtccagcggcgtggcctctgactcatctccagtggtttgtcacctctggccctgttcctgtcattccctatttgtgtgctatctctaagcctgacgtggttttcctcctgtcaaaagtacaccactacag
//

Annotations:

ANNOTATIONS from NCBI Entrez Gene (20130726):
            GeneID:8930 -> Molecular function: GO:0003696 [satellite DNA binding] evidence: TAS
            GeneID:8930 -> Molecular function: GO:0004520 [endodeoxyribonuclease activity] evidence: TAS
            GeneID:8930 -> Molecular function: GO:0005515 [protein binding] evidence: IPI
            GeneID:8930 -> Molecular function: GO:0008263 [pyrimidine-specific mismatch base pair DNA N-glycosylase activity] evidence: IDA
            GeneID:8930 -> Biological process: GO:0006281 [DNA repair] evidence: TAS
            GeneID:8930 -> Biological process: GO:0006284 [base-excision repair] evidence: TAS
            GeneID:8930 -> Biological process: GO:0006285 [base-excision repair, AP site formation] evidence: TAS
            GeneID:8930 -> Biological process: GO:0008630 [intrinsic apoptotic signaling pathway in response to DNA damage] evidence: IEA
            GeneID:8930 -> Biological process: GO:0009314 [response to radiation] evidence: IEA
            GeneID:8930 -> Biological process: GO:0031572 [G2 DNA damage checkpoint] evidence: IEA
            GeneID:8930 -> Biological process: GO:0045008 [depyrimidination] evidence: TAS
            GeneID:8930 -> Cellular component: GO:0000785 [chromatin] evidence: IEA
            GeneID:8930 -> Cellular component: GO:0005634 [nucleus] evidence: IDA
            GeneID:8930 -> Cellular component: GO:0005654 [nucleoplasm] evidence: TAS
            GeneID:8930 -> Cellular component: GO:0005730 [nucleolus] evidence: IDA
            GeneID:8930 -> Cellular component: GO:0005737 [cytoplasm] evidence: IEA

by @meso_cacase at DBCLS
This page is licensed under a Creative Commons Attribution 2.1 Japan License.