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Aliases for BCDIN3D Gene

Aliases for BCDIN3D Gene

  • BCDIN3 Domain Containing RNA Methyltransferase 2 3 5
  • BCDIN3 Domain-Containing Protein 3 4
  • BCDIN3 Domain Containing RNA Methyltransfease 3
  • Pre-MiRNA 5-Monophosphate Methyltransferase 3
  • Probable Methyltransferase BCDIN3D 3
  • BCDIN3 Domain Containing 2
  • EC 2.1.1.- 4

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. Gene Ontology (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.

Additional gene information for BCDIN3D Gene

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

GeneHancer (GH) Regulatory Elements for BCDIN3D Gene

Promoters and enhancers for BCDIN3D Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J049841 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 674.9 +0.3 294 2.6 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF143 KLF13 SP3 BCDIN3D DDX23 SMARCD1 KMT2D LMBR1L ATF1 LIMA1 CCDC65 FAIM2 NCKAP5L
GH12J048865 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 86.5 +976.9 976899 2.2 HDGF PKNOX1 FOXA2 ZFP64 ARID4B SIN3A FEZF1 ZNF2 YY1 SLC30A9 RND1 DDX23 KMT2D KANSL2 CCNT1 LOC390314 LMBR1L SENP1 BCDIN3D PRPF40B
GH12J049263 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 72.6 +576.6 576600 6.6 CLOCK DMAP1 YY1 ZNF213 ZNF143 ZNF263 SP3 NFYC ZFP41 MEF2D TUBA1C ENSG00000258101 DDX23 KMT2D CCNT1 LMBR1L SMARCD1 LOC390314 KANSL2 BCDIN3D
GH12J049129 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 69.4 +711.8 711762 4.6 CLOCK MLX FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 E2F8 GC12M049133 TUBA1B ENSG00000200309 DDX23 LMBR1L SMARCD1 KMT2D LOC390314 KANSL2 BCDIN3D
GH12J050399 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 52.9 -558.8 -558754 4 DMAP1 YY1 SLC30A9 E2F8 ZNF143 ZNF548 SP3 ZNF610 ZNF585B NBN GC12M050402 LARP4 SMARCD1 LIMA1 BCDIN3D PRPF40B ATF1 ENSG00000257298 ENSG00000257964 LOC100422296
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BCDIN3D on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BCDIN3D gene promoter:
  • Bach1
  • Msx-1
  • SREBP-1c
  • SREBP-1b
  • SREBP-1a
  • HTF
  • IRF-7A
  • HOXA3
  • GATA-1
  • C/EBPalpha

Genomic Locations for BCDIN3D Gene

Genomic Locations for BCDIN3D Gene
chr12:49,836,039-49,843,129
(GRCh38/hg38)
Size:
7,091 bases
Orientation:
Minus strand
chr12:50,229,826-50,236,912
(GRCh37/hg19)
Size:
7,087 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

Post-translational modifications for BCDIN3D Gene

  • Ubiquitination at posLast=143143
  • Modification sites at PhosphoSitePlus

Other Protein References for BCDIN3D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for BCDIN3D Gene

Domains & Families for BCDIN3D Gene

Gene 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

Phenotypes From GWAS Catalog 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 EXP,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
genes like me logo Genes that share phenotypes with BCDIN3D: view

Animal Model Products

miRNA for BCDIN3D Gene

miRTarBase miRNAs that target BCDIN3D

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleus (3)
See all subcellular structures

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 TAS --
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,TAS --
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:

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

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 33
  • 99.54 (n)
OneToOne
dog
(Canis familiaris)
Mammalia BCDIN3D 34 33
  • 88.74 (n)
OneToOne
cow
(Bos Taurus)
Mammalia BCDIN3D 34 33
  • 88.58 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Bcdin3d 33
  • 82.97 (n)
mouse
(Mus musculus)
Mammalia Bcdin3d 16 34 33
  • 81.68 (n)
oppossum
(Monodelphis domestica)
Mammalia BCDIN3D 34
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia BCDIN3D 34
  • 51 (a)
OneToOne
chicken
(Gallus gallus)
Aves BCDIN3D 34 33
  • 66.93 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia BCDIN3D 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia bcdin3d 33
  • 60.36 (n)
Str.4217 33
African clawed frog
(Xenopus laevis)
Amphibia MGC69172 33
zebrafish
(Danio rerio)
Actinopterygii LOC568375 33
  • 56.54 (n)
bcdin3d 34
  • 48 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9002 33
fruit fly
(Drosophila melanogaster)
Insecta CG11342 34 33
  • 46.42 (n)
OneToOne
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)
Aminode:
Evolutionary constrained regions (ECRs) for BCDIN3D: view image

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 Variation AA Info Type
rs143608766 likely-benign, Oromandibular-limb hypogenesis spectrum 49,843,065(-) T/C coding_sequence_variant, missense_variant
rs1000020027 -- 49,837,181(-) G/A 3_prime_UTR_variant
rs1000120556 -- 49,844,336(-) A/G upstream_transcript_variant
rs1000339377 -- 49,842,888(-) G/A coding_sequence_variant, missense_variant
rs1000393141 -- 49,842,553(-) C/G 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)

Additional Variant Information 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

Additional Disease Information for BCDIN3D

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

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 58
  2. Analyses of shared genetic factors between asthma and obesity in children. (PMID: 20816195) Melén E … Lasky-Su J (The Journal of allergy and clinical immunology 2010) 3 44 58
  3. 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 RJ (Diabetes 2010) 3 44 58
  4. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweight Collaborative study. (PMID: 20712903) Morgan AR … Mitchell EA (BMC medical genetics 2010) 3 44 58
  5. 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 MC … Ma RC (The Journal of clinical endocrinology and metabolism 2010) 3 44 58

Products for BCDIN3D Gene

Sources for BCDIN3D Gene

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