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Aliases for BCDIN3D Gene

Aliases for BCDIN3D Gene

  • BCDIN3 Domain Containing RNA Methyltransferase 2 3 5
  • BCDIN3 Domain-Containing Protein 4
  • BCDIN3 Domain Containing 2
  • EC 2.1.1.- 4
  • EC 2.1.1 61

External Ids for BCDIN3D Gene

Previous GeneCards Identifiers for BCDIN3D Gene

  • GC12M048518
  • GC12M050231
  • GC12M047260

Summaries for BCDIN3D Gene

Entrez Gene Summary for BCDIN3D Gene

  • 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]

GeneCards Summary for BCDIN3D Gene

BCDIN3D (BCDIN3 Domain Containing RNA Methyltransferase) is a Protein Coding gene. GO annotations related to this gene include methyltransferase activity and RNA methyltransferase activity.

UniProtKB/Swiss-Prot for BCDIN3D Gene

  • 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.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BCDIN3D Gene

Genomics for BCDIN3D Gene

Regulatory Elements for BCDIN3D Gene

Enhancers for BCDIN3D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12G049129 1.5 ENCODE dbSUPER 22.2 +711.8 711763 4.6 MLX CREB3L1 AGO1 DMAP1 YBX1 FEZF1 YY1 SLC30A9 ZNF416 ZNF143 LOC390314 DDX23 CCNT1 KANSL2 PRPF40B LOC105369760 BCDIN3D OR5BK1P CCDC184 LOC100422296
GH12G050688 1.1 dbSUPER 23.9 -846.4 -846441 1.4 HDGF CREB3L1 SIN3A ZNF2 YY1 ZNF766 ZNF143 ZNF207 ZNF263 SP3 BCDIN3D ATF1 CERS5 RNU6-769P LIMA1 DIP2B GC12M050681 GC12P050744
GH12G050246 1.6 Ensembl ENCODE dbSUPER 14 -408.3 -408322 10.5 HDGF FOXA2 PKNOX1 ARNT SIN3A FEZF1 ZNF2 ZNF143 FOS SP3 ENSG00000257298 PRPF40B CERS5 LIMA1 BCDIN3D ATF1 LOC100422296 PRPH ENSG00000257964 TFCP2
GH12G049661 2 FANTOM5 Ensembl ENCODE dbSUPER 10.9 +179.4 179362 4.9 HDGF PKNOX1 CREB3L1 ARID4B SIN3A ZNF2 ZBTB7B ZNF766 ZNF302 ZNF143 DDX23 LOC390314 KANSL2 LIMA1 CCNT1 ENSG00000257298 FMNL3 LOC101927267 MCRS1 BCDIN3D-AS1
GH12G049344 1.7 FANTOM5 Ensembl ENCODE 12.7 +496.3 496305 4.4 MLX DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 NFYC TBX21 DDX23 CCNT1 LOC390314 KANSL2 LIMA1 PRPF40B BCDIN3D LOC101927267 DNAJC22 ENSG00000257298
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around BCDIN3D on UCSC Golden Path with GeneCards custom track

Promoters for BCDIN3D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000051682 429 1401 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 FOS SP3 ZHX2 REST

Genomic Location for BCDIN3D Gene

Chromosome:
12
Start:
49,836,039 bp from pter
End:
49,843,129 bp from pter
Size:
7,091 bases
Orientation:
Minus strand

Genomic View for BCDIN3D Gene

Genes around BCDIN3D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BCDIN3D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BCDIN3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BCDIN3D Gene

Proteins for BCDIN3D Gene

  • Protein details for BCDIN3D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z5W3-BN3D2_HUMAN
    Recommended name:
    Pre-miRNA 5-monophosphate methyltransferase
    Protein Accession:
    Q7Z5W3
    Secondary Accessions:
    • A8K829

    Protein attributes for BCDIN3D Gene

    Size:
    292 amino acids
    Molecular mass:
    33200 Da
    Quaternary structure:
    • Interacts with DICER1; the interaction may be mediated by RNA.

neXtProt entry for BCDIN3D Gene

Selected DME Specific Peptides for BCDIN3D Gene

Q7Z5W3:
  • WDRSLLLFR
  • LSSFLSQFGRSVFD
  • YLLVEPQPWKCYRAAARRLRKLGLH
  • ILTQDHGMEL

Post-translational modifications for BCDIN3D Gene

  • Ubiquitination at Lys143
  • Modification sites at PhosphoSitePlus

Other Protein References for BCDIN3D Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for BCDIN3D Gene

Protein Domains for BCDIN3D Gene

Suggested Antigen Peptide Sequences for BCDIN3D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q7Z5W3

UniProtKB/Swiss-Prot:

BN3D2_HUMAN :
  • Belongs to the methyltransferase superfamily.
Family:
  • Belongs to the methyltransferase superfamily.
genes like me logo Genes that share domains with BCDIN3D: view

Function for BCDIN3D Gene

Molecular function for BCDIN3D Gene

UniProtKB/Swiss-Prot 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.

Enzyme Numbers (IUBMB) for BCDIN3D Gene

Gene Ontology (GO) - Molecular Function for BCDIN3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0008168 methyltransferase activity IEA --
GO:0008171 O-methyltransferase activity IDA 23063121
GO:0008173 RNA methyltransferase activity IDA 23063121
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with BCDIN3D: view

Phenotypes for BCDIN3D Gene

genes like me logo Genes that share phenotypes with BCDIN3D: view

Animal Model Products

miRNA for BCDIN3D Gene

miRTarBase miRNAs that target BCDIN3D

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for BCDIN3D Gene

Localization for BCDIN3D Gene

Subcellular locations from UniProtKB/Swiss-Prot for BCDIN3D Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for BCDIN3D gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for BCDIN3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005737 cytoplasm IDA,IEA 23063121
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with BCDIN3D: view

Pathways & Interactions for BCDIN3D Gene

SuperPathways for BCDIN3D Gene

No Data Available

Interacting Proteins for BCDIN3D Gene

Gene Ontology (GO) - Biological Process for BCDIN3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001510 RNA methylation IDA 23063121
GO:0010586 miRNA metabolic process IDA 23063121
GO:0032259 methylation IEA --
GO:2000632 negative regulation of pre-miRNA processing IDA 23063121
genes like me logo Genes that share ontologies with BCDIN3D: view

No data available for Pathways by source and SIGNOR curated interactions for BCDIN3D Gene

Drugs & Compounds for BCDIN3D Gene

No Compound Related Data Available

Transcripts for BCDIN3D Gene

mRNA/cDNA for BCDIN3D Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(61) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for BCDIN3D Gene

BCDIN3 domain containing:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for BCDIN3D Gene

No ASD Table

Relevant External Links for BCDIN3D Gene

GeneLoc Exon Structure for
BCDIN3D
ECgene alternative splicing isoforms for
BCDIN3D

Expression for BCDIN3D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BCDIN3D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for BCDIN3D Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for BCDIN3D Gene



Protein tissue co-expression partners for BCDIN3D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of BCDIN3D Gene:

BCDIN3D

SOURCE GeneReport for Unigene cluster for BCDIN3D Gene:

Hs.142736

Evidence on tissue expression from TISSUES for BCDIN3D Gene

  • Skin(4.1)
genes like me logo Genes that share expression patterns with BCDIN3D: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for BCDIN3D Gene

Orthologs for BCDIN3D Gene

This gene was present in the common ancestor of animals.

Orthologs for BCDIN3D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia BCDIN3D 34 35
  • 99.54 (n)
dog
(Canis familiaris)
Mammalia BCDIN3D 34 35
  • 88.74 (n)
cow
(Bos Taurus)
Mammalia BCDIN3D 34 35
  • 88.58 (n)
rat
(Rattus norvegicus)
Mammalia Bcdin3d 34
  • 82.97 (n)
mouse
(Mus musculus)
Mammalia Bcdin3d 34 16 35
  • 81.68 (n)
oppossum
(Monodelphis domestica)
Mammalia BCDIN3D 35
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia BCDIN3D 35
  • 51 (a)
OneToOne
chicken
(Gallus gallus)
Aves BCDIN3D 34 35
  • 66.93 (n)
lizard
(Anolis carolinensis)
Reptilia BCDIN3D 35
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia bcdin3d 34
  • 60.36 (n)
Str.4217 34
African clawed frog
(Xenopus laevis)
Amphibia MGC69172 34
zebrafish
(Danio rerio)
Actinopterygii LOC568375 34
  • 56.54 (n)
bcdin3d 35
  • 48 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9002 34
fruit fly
(Drosophila melanogaster)
Insecta CG11342 34 35
  • 46.42 (n)
Species where no ortholog for BCDIN3D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for BCDIN3D Gene

ENSEMBL:
Gene Tree for BCDIN3D (if available)
TreeFam:
Gene Tree for BCDIN3D (if available)

Paralogs for BCDIN3D Gene

No data available for Paralogs for BCDIN3D Gene

Variants for BCDIN3D Gene

Sequence variations from dbSNP and Humsavar for BCDIN3D Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs143608766 Likely benign 49,843,065(+) CTCCA(C/T)CCAGT reference, missense
rs1000020027 -- 49,837,181(+) ACTAA(A/G)GGATA intron-variant, utr-variant-3-prime
rs1000120556 -- 49,844,336(+) CAAAC(A/G)GTACC upstream-variant-2KB
rs1000339377 -- 49,842,888(+) GAATC(A/G)GCCCG reference, missense
rs1000393141 -- 49,842,553(+) CCAGC(C/G)AAAGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for BCDIN3D Gene

Variant ID Type Subtype PubMed ID
nsv522972 CNV gain 19592680

Variation tolerance for BCDIN3D Gene

Residual Variation Intolerance Score: 49.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.96; 79.84% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for BCDIN3D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
BCDIN3D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for BCDIN3D Gene

Disorders for BCDIN3D Gene

Relevant External Links for BCDIN3D

Genetic Association Database (GAD)
BCDIN3D
Human Genome Epidemiology (HuGE) Navigator
BCDIN3D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
BCDIN3D

No disorders were found for BCDIN3D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for BCDIN3D Gene

Publications for BCDIN3D Gene

  1. Human RNA methyltransferase BCDIN3D regulates microRNA processing. (PMID: 23063121) Xhemalce B. … Kouzarides T. (Cell 2012) 2 3 4 64
  2. Implication of genetic variants near NEGR1, SEC16B, TMEM18, ETV5/DGKG, GNPDA2, LIN7C/BDNF, MTCH2, BCDIN3D/FAIM2, SH2B1, FTO, MC4R, and KCTD15 with obesity and type 2 diabetes in 7705 Chinese. (PMID: 20215397) Ng M.C. … Ma R.C. (J. Clin. Endocrinol. Metab. 2010) 3 46 64
  3. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweight Collaborative study. (PMID: 20712903) Morgan A.R. … Mitchell E.A. (BMC Med. Genet. 2010) 3 46 64
  4. Genetic susceptibility to obesity and related traits in childhood and adolescence: influence of loci identified by genome-wide association studies. (PMID: 20724581) den Hoed M. … Loos R.J. (Diabetes 2010) 3 46 64
  5. Analyses of shared genetic factors between asthma and obesity in children. (PMID: 20816195) MelAcn E. … Lasky-Su J. (J. Allergy Clin. Immunol. 2010) 3 46 64

Products for BCDIN3D Gene

Sources for BCDIN3D Gene

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