Bcdin3d (BCDIN3 domain containing RNA methyltransferase) - Rat Genome Database

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Gene: Bcdin3d (BCDIN3 domain containing RNA methyltransferase) Rattus norvegicus
Analyze
Symbol: Bcdin3d
Name: BCDIN3 domain containing RNA methyltransferase
RGD ID: 1306433
Description: Predicted to enable pre-miRNA binding activity; small RNA 2'-O-methyltransferase activity; and tRNA methyltransferase activity. Predicted to be involved in negative regulation of pre-miRNA processing; pre-miRNA processing; and tRNA methylation. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in cytoplasm. Orthologous to human BCDIN3D (BCDIN3 domain containing RNA methyltransferase); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: BCDIN3 domain containing; BCDIN3 domain containing RNA methyltransfease; BCDIN3 domain-containing protein; LOC363001; pre-miRNA 5'-monophosphate methyltransferase; probable methyltransferase BCDIN3D; RGD1306433; RNA 5'-monophosphate methyltransferase; similar to RIKEN cDNA 4930556P03
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87132,484,404 - 132,488,998 (-)NCBIGRCr8
mRatBN7.27130,605,540 - 130,610,134 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7130,605,541 - 130,610,115 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7132,408,793 - 132,413,362 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07134,634,376 - 134,638,941 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07134,546,889 - 134,551,454 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07141,132,106 - 141,136,700 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7141,132,133 - 141,136,700 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X115,635,386 - 115,639,979 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47138,218,542 - 138,223,136 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17138,295,005 - 138,299,552 (-)NCBI
Celera7127,087,893 - 127,092,463 (-)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA,ISO,ISS)
cytosol  (IEA,ISO)
nucleoplasm  (IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:23063121   PMID:28119416   PMID:31919512  


Genomics

Comparative Map Data
Bcdin3d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87132,484,404 - 132,488,998 (-)NCBIGRCr8
mRatBN7.27130,605,540 - 130,610,134 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7130,605,541 - 130,610,115 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7132,408,793 - 132,413,362 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07134,634,376 - 134,638,941 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07134,546,889 - 134,551,454 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07141,132,106 - 141,136,700 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7141,132,133 - 141,136,700 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X115,635,386 - 115,639,979 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47138,218,542 - 138,223,136 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17138,295,005 - 138,299,552 (-)NCBI
Celera7127,087,893 - 127,092,463 (-)NCBICelera
Cytogenetic Map7q36NCBI
BCDIN3D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381249,836,043 - 49,843,106 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1249,836,043 - 49,843,106 (-)EnsemblGRCh38hg38GRCh38
GRCh371250,229,826 - 50,236,889 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361248,517,823 - 48,523,142 (-)NCBINCBI36Build 36hg18NCBI36
Celera1249,025,845 - 49,032,931 (-)NCBICelera
Cytogenetic Map12q13.12NCBI
HuRef1247,260,836 - 47,267,922 (-)NCBIHuRef
CHM1_11250,196,151 - 50,203,237 (-)NCBICHM1_1
T2T-CHM13v2.01249,799,057 - 49,806,118 (-)NCBIT2T-CHM13v2.0
Bcdin3d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391599,367,965 - 99,372,611 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1599,367,960 - 99,372,611 (-)EnsemblGRCm39 Ensembl
GRCm381599,470,084 - 99,474,730 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1599,470,079 - 99,474,730 (-)EnsemblGRCm38mm10GRCm38
MGSCv371599,300,515 - 99,305,161 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361599,298,118 - 99,302,763 (-)NCBIMGSCv36mm8
Celera15101,625,365 - 101,630,003 (-)NCBICelera
Cytogenetic Map15F1NCBI
cM Map1556.13NCBI
Bcdin3d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955547427,432 - 432,455 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955547427,127 - 432,482 (-)NCBIChiLan1.0ChiLan1.0
BCDIN3D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21044,338,069 - 44,348,851 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11244,334,821 - 44,347,456 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01238,907,254 - 38,913,958 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11239,802,601 - 39,807,948 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1239,802,601 - 39,807,948 (+)Ensemblpanpan1.1panPan2
BCDIN3D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1274,851,156 - 4,860,322 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl274,851,063 - 4,855,945 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2741,399,538 - 41,406,533 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0274,900,535 - 4,907,530 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl274,900,390 - 4,905,300 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1274,866,116 - 4,873,088 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0274,855,524 - 4,862,527 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02741,794,412 - 41,801,407 (-)NCBIUU_Cfam_GSD_1.0
Bcdin3d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494565,643,738 - 65,651,357 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365127,514,348 - 7,521,017 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365127,516,324 - 7,521,063 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BCDIN3D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl515,751,312 - 15,761,537 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1515,755,307 - 15,761,645 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2516,197,466 - 16,203,648 (+)NCBISscrofa10.2Sscrofa10.2susScr3
BCDIN3D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11146,076,225 - 46,082,018 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1146,076,827 - 46,081,784 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037200,041,421 - 200,048,446 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Bcdin3d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248162,447,739 - 2,453,228 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248162,447,703 - 2,455,543 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Bcdin3d
11 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:293
Count of miRNA genes:182
Interacting mature miRNAs:212
Transcripts:ENSRNOT00000043408
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

Markers in Region
RH134395  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27130,605,759 - 130,605,973 (+)MAPPERmRatBN7.2
Rnor_6.07141,132,326 - 141,132,539NCBIRnor6.0
Rnor_5.0X115,635,606 - 115,635,819UniSTSRnor5.0
RGSC_v3.47138,218,762 - 138,218,975UniSTSRGSC3.4
Celera7127,088,113 - 127,088,326UniSTS
RH 3.4 Map71077.3UniSTS
Cytogenetic Map7q36UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 2 8 2 9 2 50 12 27 5
Low 2 41 49 39 10 39 8 11 24 23 14 6 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000091538   ⟹   ENSRNOP00000070196
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7130,605,541 - 130,610,115 (-)Ensembl
Rnor_6.0 Ensembl7141,132,133 - 141,136,700 (-)Ensembl
RefSeq Acc Id: NM_001108751   ⟹   NP_001102221
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87132,484,404 - 132,488,998 (-)NCBI
mRatBN7.27130,605,540 - 130,610,134 (-)NCBI
Rnor_6.07141,132,106 - 141,136,700 (-)NCBI
Rnor_5.0X115,635,386 - 115,639,979 (-)NCBI
RGSC_v3.47138,218,542 - 138,223,136 (-)RGD
Celera7127,087,893 - 127,092,463 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102221 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D4ABH7 (Get FASTA)   NCBI Sequence Viewer  
  EDL86984 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000070196
  ENSRNOP00000070196.1
  ENSRNOP00055041948
  ENSRNOP00060007887
  ENSRNOP00065029776
Reference Protein Sequences
RefSeq Acc Id: NP_001102221   ⟸   NM_001108751
- UniProtKB: D4ABH7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070196   ⟸   ENSRNOT00000091538
Protein Domains
Bin3-type SAM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ABH7-F1-model_v2 AlphaFold D4ABH7 1-285 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13695643
Promoter ID:EPDNEW_R6168
Type:single initiation site
Name:Bcdin3d_1
Description:BCDIN3 domain containing RNA methyltransferase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07141,136,688 - 141,136,748EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306433 AgrOrtholog
BioCyc Gene G2FUF-32069 BioCyc
Ensembl Genes ENSRNOG00000058430 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055029395 UniProtKB/Swiss-Prot
  ENSRNOG00060006497 UniProtKB/Swiss-Prot
  ENSRNOG00065021746 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000091538 ENTREZGENE
  ENSRNOT00000091538.2 UniProtKB/Swiss-Prot
  ENSRNOT00055050923 UniProtKB/Swiss-Prot
  ENSRNOT00060010642 UniProtKB/Swiss-Prot
  ENSRNOT00065036963 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.150 UniProtKB/Swiss-Prot
InterPro Bin3-like UniProtKB/Swiss-Prot
  Bin3_C UniProtKB/Swiss-Prot
  BIN3_SAM-bd_dom UniProtKB/Swiss-Prot
  SAM-dependent_MTases UniProtKB/Swiss-Prot
KEGG Report rno:363001 UniProtKB/Swiss-Prot
NCBI Gene 363001 ENTREZGENE
PANTHER PTHR12315 UniProtKB/Swiss-Prot
  RNA 5'-MONOPHOSPHATE METHYLTRANSFERASE UniProtKB/Swiss-Prot
Pfam Bin3 UniProtKB/Swiss-Prot
PhenoGen Bcdin3d PhenoGen
PROSITE BIN3_SAM UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000058430 RatGTEx
  ENSRNOG00055029395 RatGTEx
  ENSRNOG00060006497 RatGTEx
  ENSRNOG00065021746 RatGTEx
Superfamily-SCOP SSF53335 UniProtKB/Swiss-Prot
UniProt BN3D2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-15 Bcdin3d  BCDIN3 domain containing RNA methyltransferase  Bcdin3d  BCDIN3 domain containing RNA methyltransfease  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-12-02 Bcdin3d  BCDIN3 domain containing RNA methyltransfease  Bcdin3d  BCDIN3 domain containing  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Bcdin3d  BCDIN3 domain containing  RGD1306433_predicted  similar to RIKEN cDNA 4930556P03 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1306433_predicted  similar to RIKEN cDNA 4930556P03 (predicted)  LOC363001_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC363001_predicted  similar to RIKEN cDNA 4930556P03 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL