Human Gene BCDIN3D (uc001rvh.3) Description and Page Index
  Description: Homo sapiens BCDIN3 domain containing (BCDIN3D), mRNA.
RefSeq Summary (NM_181708): This gene encodes an RNA methyltransferase which belongs to the rossmann fold methyltransferase family, and serves as a 5'-methylphosphate capping enzyme that is specific for cytoplasmic histidyl tRNA. The encoded protein contains an S-adenosylmethionine binding domain and uses the methyl group donor, S-adenosylmethionine. This gene is overexpressed in breast cancer cells, and is related to the tumorigenic phenotype and poor prognosis of breast cancer. The encoded protein is thought to promote the cellular invasion of breast cancer cells, by downregulating the expression of tumor suppressor miRNAs through the dimethylation of the 5-monophosphate of the corresponding precursor miRNAs. [provided by RefSeq, Apr 2017]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. ##Evidence-Data-START## Transcript exon combination :: SRR1660805.55522.1, SRR1803615.264520.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000333924.6/ ENSP00000335201.4 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr12:50,229,826-50,236,912 Size: 7,087 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr12:50,232,154-50,236,870 Size: 4,717 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:50,229,826-50,236,912)mRNA (may differ from genome)Protein (292 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtPubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Pre-miRNA 5'-monophosphate methyltransferase; EC=2.1.1.-; AltName: Full=BCDIN3 domain-containing protein;
FUNCTION: O-methyltransferase that specifically dimethylates the 5' monophosphate of pre-miRNAs, acting as a negative regulator of miRNA processing. The 5' monophosphate of pre-miRNAs is recognized by DICER1 and is required for pre-miRNAs processing: methylation at this position reduces the processing of pre-miRNAs by DICER1. Able to mediate methylation of pre-miR-145, as well as other pre- miRNAs.
SUBUNIT: Interacts with DICER1; the interaction may be mediated by RNA.
SIMILARITY: Belongs to the methyltransferase superfamily.
SIMILARITY: Contains 1 Bin3-type SAM domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): BCDIN3D
CDC HuGE Published Literature: BCDIN3D
Positive Disease Associations: Body mass index , Body Weight , waist circumference , weight
Related Studies:
  1. Body mass index
    Thorleifsson ,et al. 2008, Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity, Nature genetics 2009 41- 1 : 18-24. [PubMed 19079260]
  2. Body Mass Index
    Gudmar Thorleifsson et al. Nature genetics 2009, Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity., Nature genetics. [PubMed 19079260]
  3. Body Mass Index
    Elizabeth K Speliotes et al. Nature genetics 2010, Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index., Nature genetics. [PubMed 20935630]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.22 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 159.69 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -16.8042-0.400 Picture PostScript Text
3' UTR -690.242328-0.296 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR010675 - Bin3
IPR024160 - BIN3_SAM-bd_dom

Pfam Domains:
PF06859 - Bicoid-interacting protein 3 (Bin3)

SCOP Domains:
53335 - S-adenosyl-L-methionine-dependent methyltransferases

ModBase Predicted Comparative 3D Structure on Q7Z5W3
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  Protein SequenceProtein Sequence  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008171 O-methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0016740 transferase activity

Biological Process:
GO:0001510 RNA methylation
GO:0010586 miRNA metabolic process
GO:0032259 methylation
GO:2000632 negative regulation of pre-miRNA processing

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

-  Descriptions from all associated GenBank mRNAs
  JD138239 - Sequence 119263 from Patent EP1572962.
JD066629 - Sequence 47653 from Patent EP1572962.
JD073064 - Sequence 54088 from Patent EP1572962.
JD444797 - Sequence 425821 from Patent EP1572962.
JD211796 - Sequence 192820 from Patent EP1572962.
JD511618 - Sequence 492642 from Patent EP1572962.
JD247028 - Sequence 228052 from Patent EP1572962.
JD413454 - Sequence 394478 from Patent EP1572962.
JD198147 - Sequence 179171 from Patent EP1572962.
JD212753 - Sequence 193777 from Patent EP1572962.
JD542773 - Sequence 523797 from Patent EP1572962.
JD537358 - Sequence 518382 from Patent EP1572962.
JD247027 - Sequence 228051 from Patent EP1572962.
BC053560 - Homo sapiens BCDIN3 domain containing, mRNA (cDNA clone MGC:61656 IMAGE:6163678), complete cds.
BC040957 - Homo sapiens BCDIN3 domain containing, mRNA (cDNA clone IMAGE:5722801).
AK292194 - Homo sapiens cDNA FLJ75785 complete cds.
JD552268 - Sequence 533292 from Patent EP1572962.
JD260118 - Sequence 241142 from Patent EP1572962.
JD433412 - Sequence 414436 from Patent EP1572962.
JD355160 - Sequence 336184 from Patent EP1572962.
JD511251 - Sequence 492275 from Patent EP1572962.
JD545935 - Sequence 526959 from Patent EP1572962.
JD146024 - Sequence 127048 from Patent EP1572962.
JD206653 - Sequence 187677 from Patent EP1572962.
JD047260 - Sequence 28284 from Patent EP1572962.
JD515071 - Sequence 496095 from Patent EP1572962.
JD047259 - Sequence 28283 from Patent EP1572962.
JD553364 - Sequence 534388 from Patent EP1572962.
JD317168 - Sequence 298192 from Patent EP1572962.
CU690986 - Synthetic construct Homo sapiens gateway clone IMAGE:100021701 5' read BCDIN3D mRNA.
HQ448096 - Synthetic construct Homo sapiens clone IMAGE:100071476; CCSB011908_01 BCDIN3 domain containing (BCDIN3D) gene, encodes complete protein.
KJ895575 - Synthetic construct Homo sapiens clone ccsbBroadEn_04969 BCDIN3D gene, encodes complete protein.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q7Z5W3 (Reactome details) participates in the following event(s):

R-HSA-5578717 BCDIN3D dimethylates 5' phosphate of pre-miR-145
R-HSA-203927 MicroRNA (miRNA) biogenesis
R-HSA-211000 Gene Silencing by RNA
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A8K829, BN3D2_HUMAN, NM_181708, NP_859059, Q7Z5W3
UCSC ID: uc001rvh.3
RefSeq Accession: NM_181708
Protein: Q7Z5W3 (aka BN3D2_HUMAN)
CCDS: CCDS8790.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_181708.2
exon count: 2CDS single in 3' UTR: no RNA size: 3266
ORF size: 879CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1943.00frame shift in genome: no % Coverage: 99.48
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.