Rbm11 (RNA binding motif protein 11) - Rat Genome Database

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Gene: Rbm11 (RNA binding motif protein 11) Rattus norvegicus
Analyze
Symbol: Rbm11
Name: RNA binding motif protein 11
RGD ID: 1305195
Description: Predicted to enable poly(U) RNA binding activity and protein homodimerization activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome. Predicted to act upstream of or within cellular response to oxidative stress. Predicted to be located in nuclear speck. Predicted to be active in nucleus. Orthologous to human RBM11 (RNA binding motif protein 11); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC288321; splicing regulator RBM11
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
GRCr81127,721,870 - 27,731,125 (+)NCBIGRCr8
mRatBN7.21114,234,851 - 14,244,092 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1114,234,890 - 14,244,090 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1122,859,949 - 22,869,159 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01115,586,333 - 15,595,543 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01114,754,201 - 14,763,411 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01114,005,704 - 14,015,723 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1114,005,732 - 14,014,962 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01117,664,383 - 17,674,391 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41114,381,923 - 14,391,904 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11114,379,374 - 14,390,086 (+)NCBI
Celera1114,248,500 - 14,258,481 (+)NCBICelera
Cytogenetic Map11p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nuclear speck  (ISO)
nucleoplasm  (ISO)
nucleus  (IBA,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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:21984414  


Genomics

Comparative Map Data
Rbm11
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81127,721,870 - 27,731,125 (+)NCBIGRCr8
mRatBN7.21114,234,851 - 14,244,092 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1114,234,890 - 14,244,090 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1122,859,949 - 22,869,159 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01115,586,333 - 15,595,543 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01114,754,201 - 14,763,411 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01114,005,704 - 14,015,723 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1114,005,732 - 14,014,962 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01117,664,383 - 17,674,391 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41114,381,923 - 14,391,904 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11114,379,374 - 14,390,086 (+)NCBI
Celera1114,248,500 - 14,258,481 (+)NCBICelera
Cytogenetic Map11p11NCBI
RBM11
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382114,216,157 - 14,228,372 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2114,216,130 - 14,228,372 (+)EnsemblGRCh38hg38GRCh38
GRCh372115,588,478 - 15,600,693 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362114,510,350 - 14,522,552 (+)NCBINCBI36Build 36hg18NCBI36
Build 342114,510,349 - 14,522,552NCBI
Celera21745,717 - 757,944 (+)NCBICelera
Cytogenetic Map21q11.2NCBI
HuRef21958,833 - 971,058 (+)NCBIHuRef
CHM1_12115,148,999 - 15,161,227 (+)NCBICHM1_1
T2T-CHM13v2.02112,558,865 - 12,571,078 (+)NCBIT2T-CHM13v2.0
Rbm11
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391675,389,796 - 75,399,706 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1675,389,732 - 75,399,717 (+)EnsemblGRCm39 Ensembl
GRCm381675,592,844 - 75,602,825 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1675,592,844 - 75,602,829 (+)EnsemblGRCm38mm10GRCm38
MGSCv371675,593,136 - 75,603,070 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361675,475,524 - 75,484,382 (+)NCBIMGSCv36mm8
Celera1675,829,936 - 75,839,869 (+)NCBICelera
Cytogenetic Map16C3.1NCBI
cM Map1643.22NCBI
Rbm11
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540716,071,208 - 16,081,949 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540716,071,186 - 16,082,332 (+)NCBIChiLan1.0ChiLan1.0
RBM11
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22210,693,134 - 10,705,375 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1215,526,875 - 5,538,726 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v021942,533 - 954,775 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12114,309,922 - 14,322,142 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2114,309,883 - 14,322,142 (+)Ensemblpanpan1.1panPan2
RBM11
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13111,204,273 - 11,217,526 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3111,203,207 - 11,217,509 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3111,215,073 - 11,228,492 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03111,228,501 - 11,241,994 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3111,228,404 - 11,241,994 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13111,201,584 - 11,215,096 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03111,239,110 - 11,252,365 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03111,635,470 - 11,648,982 (+)NCBIUU_Cfam_GSD_1.0
Rbm11
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497112,327,134 - 12,337,002 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365057,246,844 - 7,256,790 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365057,246,854 - 7,256,763 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RBM11
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13179,180,467 - 179,191,924 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113179,180,611 - 179,191,934 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213189,369,722 - 189,381,248 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RBM11
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1278,390,304 - 78,395,739 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605075,603,734 - 75,618,143 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rbm11
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247452,685,372 - 2,697,518 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247452,685,445 - 2,696,791 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rbm11
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:312
Count of miRNA genes:204
Interacting mature miRNAs:234
Transcripts:ENSRNOT00000047240
Prediction methods:Microtar, Miranda, 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
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)11121836709Rat
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11135331169Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)111283104625121472Rat

Markers in Region
AW527929  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21114,243,867 - 14,244,043 (+)MAPPERmRatBN7.2
Rnor_6.01114,014,745 - 14,014,920NCBIRnor6.0
Rnor_5.01117,673,413 - 17,673,588UniSTSRnor5.0
RGSC_v3.41114,390,926 - 14,391,101UniSTSRGSC3.4
Celera1114,257,503 - 14,257,678UniSTS
Cytogenetic Map11p11UniSTS


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 11 5
Low 8 53 24
Below cutoff 2 21 9 4 14 4 4 5 10 30 12 10 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000047240   ⟹   ENSRNOP00000046624
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1114,234,890 - 14,244,090 (+)Ensembl
Rnor_6.0 Ensembl1114,005,732 - 14,014,962 (+)Ensembl
RefSeq Acc Id: NM_001401847   ⟹   NP_001388776
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81127,721,911 - 27,731,120 (+)NCBI
mRatBN7.21114,234,878 - 14,244,087 (+)NCBI
RefSeq Acc Id: XM_006247995   ⟹   XP_006248057
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81127,721,870 - 27,731,125 (+)NCBI
mRatBN7.21114,234,851 - 14,244,092 (+)NCBI
Rnor_6.01114,005,704 - 14,014,964 (+)NCBI
Rnor_5.01117,664,383 - 17,674,391 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001388776 (Get FASTA)   NCBI Sequence Viewer  
  XP_006248057 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM10578 (Get FASTA)   NCBI Sequence Viewer  
  EDM10579 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000046624.6
Reference Protein Sequences
RefSeq Acc Id: XP_006248057   ⟸   XM_006247995
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000046624   ⟸   ENSRNOT00000047240
RefSeq Acc Id: NP_001388776   ⟸   NM_001401847
Protein Domains
RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZQ24-F1-model_v2 AlphaFold D3ZQ24 1-238 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305195 AgrOrtholog
BioCyc Gene G2FUF-22234 BioCyc
Ensembl Genes ENSRNOG00000029147 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000047240.6 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RRM_RNP1 UniProtKB/TrEMBL
NCBI Gene 288321 ENTREZGENE
PANTHER RNA BINDING MOTIF RBM PROTEIN -RELATED UniProtKB/TrEMBL
  SPLICING REGULATOR RBM11 UniProtKB/TrEMBL
Pfam RRM_1 UniProtKB/TrEMBL
PhenoGen Rbm11 PhenoGen
PROSITE RRM UniProtKB/TrEMBL
RatGTEx ENSRNOG00000029147 RatGTEx
SMART RRM UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt D3ZQ24_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Rbm11  RNA binding motif protein 11   Rbm11_predicted  RNA binding motif protein 11 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Rbm11_predicted  RNA binding motif protein 11 (predicted)      Symbol and Name status set to approved 70820 APPROVED