Rbm41 (RNA binding motif protein 41) - Rat Genome Database

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Gene: Rbm41 (RNA binding motif protein 41) Rattus norvegicus
Analyze
Symbol: Rbm41
Name: RNA binding motif protein 41
RGD ID: 1590579
Description: Predicted to enable U12 snRNA binding activity and pre-mRNA intronic binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be part of U12-type spliceosomal complex. Orthologous to human RBM41 (RNA binding motif protein 41); INTERACTS WITH 17beta-estradiol; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC680581; RNA-binding protein 41; similar to CG30327-PA
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
GRCr8X108,394,323 - 108,448,969 (-)NCBIGRCr8
mRatBN7.2X103,605,732 - 103,660,381 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX103,608,585 - 103,660,381 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX105,741,077 - 105,792,881 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X109,239,805 - 109,291,617 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X106,803,396 - 106,855,166 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X111,272,347 - 111,325,203 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX111,269,490 - 111,325,186 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0353,307,343 - 53,322,777 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0353,272,291 - 53,277,434 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X127,687,341 - 127,744,248 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera344,267,369 - 44,319,103 (+)NCBICelera
Cytogenetic MapXq32NCBI
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

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

Genomics

Comparative Map Data
Rbm41
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X108,394,323 - 108,448,969 (-)NCBIGRCr8
mRatBN7.2X103,605,732 - 103,660,381 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX103,608,585 - 103,660,381 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX105,741,077 - 105,792,881 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X109,239,805 - 109,291,617 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X106,803,396 - 106,855,166 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X111,272,347 - 111,325,203 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX111,269,490 - 111,325,186 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0353,307,343 - 53,322,777 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0353,272,291 - 53,277,434 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X127,687,341 - 127,744,248 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera344,267,369 - 44,319,103 (+)NCBICelera
Cytogenetic MapXq32NCBI
RBM41
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X107,052,102 - 107,118,822 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX107,061,885 - 107,118,823 (-)EnsemblGRCh38hg38GRCh38
GRCh37X106,295,332 - 106,362,052 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X106,197,024 - 106,248,690 (-)NCBINCBI36Build 36hg18NCBI36
CeleraX106,776,426 - 106,833,365 (-)NCBICelera
Cytogenetic MapXq22.3NCBI
HuRefX95,932,996 - 95,989,584 (-)NCBIHuRef
CHM1_1X106,215,976 - 106,272,931 (-)NCBICHM1_1
T2T-CHM13v2.0X105,488,619 - 105,560,772 (-)NCBIT2T-CHM13v2.0
Rbm41
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X138,790,260 - 138,899,344 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX138,790,260 - 138,899,344 (-)EnsemblGRCm39 Ensembl
GRCm38X139,889,511 - 139,998,595 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX139,889,511 - 139,998,595 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X136,424,050 - 136,533,134 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X135,290,605 - 135,344,915 (-)NCBIMGSCv36mm8
CeleraX123,152,817 - 123,260,713 (-)NCBICelera
Cytogenetic MapXF1NCBI
cM MapX61.35NCBI
Rbm41
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554908,911,780 - 8,974,748 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554908,912,616 - 8,974,748 (+)NCBIChiLan1.0ChiLan1.0
RBM41
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X106,546,445 - 106,602,899 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X106,550,046 - 106,605,706 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X96,163,094 - 96,218,210 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X106,538,444 - 106,595,768 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX106,544,087 - 106,595,768 (-)Ensemblpanpan1.1panPan2
RBM41
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X80,648,486 - 80,704,403 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX80,651,475 - 80,704,351 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX66,767,595 - 66,823,513 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X82,291,986 - 82,347,912 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX82,293,968 - 82,347,906 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X79,754,923 - 79,810,838 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X81,466,456 - 81,522,373 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X81,258,208 - 81,314,177 (-)NCBIUU_Cfam_GSD_1.0
Rbm41
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X79,997,516 - 80,072,611 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364997,585,324 - 7,655,384 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364997,585,352 - 7,655,419 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RBM41
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX87,512,550 - 87,575,086 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X87,512,887 - 87,575,118 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X101,885,196 - 101,947,383 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RBM41
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X94,884,887 - 94,941,465 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX94,885,155 - 94,940,996 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606519,965,423 - 20,030,876 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rbm41
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248039,498,093 - 9,571,288 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248039,498,072 - 9,573,145 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rbm41
161 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:123
Count of miRNA genes:88
Interacting mature miRNAs:95
Transcripts:ENSRNOT00000068341
Prediction methods:Miranda
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
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat

Markers in Region
AU047578  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0353,283,148 - 53,283,416NCBIRnor5.0
Rnor_5.09310,612 - 310,880NCBIRnor5.0
Rnor_5.09160,942 - 161,210NCBIRnor5.0
RGSC_v3.4X127,733,123 - 127,733,390UniSTSRGSC3.4
RGSC_v3.491,697,906 - 1,698,173UniSTSRGSC3.4
Celera344,278,223 - 44,278,490UniSTS
Cytogenetic MapXq35UniSTS
BF397358  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X103,608,981 - 103,609,197 (+)MAPPERmRatBN7.2
Rnor_6.0X111,272,751 - 111,272,966NCBIRnor6.0
Rnor_5.0353,322,158 - 53,322,373UniSTSRnor5.0
RGSC_v3.4X127,687,745 - 127,687,960UniSTSRGSC3.4
Celera344,318,484 - 44,318,699UniSTS
RH 3.4 Map71122.71UniSTS
Cytogenetic MapXq35UniSTS


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 6 8 29 2 11 11
Low 2 43 51 41 11 41 8 11 45 33 27 8
Below cutoff 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000086785   ⟹   ENSRNOP00000069686
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX103,608,585 - 103,660,381 (-)Ensembl
Rnor_6.0 EnsemblX111,269,490 - 111,325,186 (-)Ensembl
RefSeq Acc Id: NM_001109420   ⟹   NP_001102890
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X108,397,169 - 108,448,969 (-)NCBI
mRatBN7.2X103,608,578 - 103,660,381 (-)NCBI
Rnor_6.0X111,272,347 - 111,325,203 (-)NCBI
Rnor_5.0353,272,291 - 53,277,434 (+)NCBI
Rnor_5.0353,307,343 - 53,322,777 (+)NCBI
RGSC_v3.4X127,687,341 - 127,744,248 (-)RGD
Celera344,267,369 - 44,319,103 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039100061   ⟹   XP_038955989
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X108,394,323 - 108,448,961 (-)NCBI
mRatBN7.2X103,605,732 - 103,660,373 (-)NCBI
RefSeq Acc Id: XM_063280300   ⟹   XP_063136370
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X108,436,250 - 108,448,965 (-)NCBI
RefSeq Acc Id: XR_010061244
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X108,400,600 - 108,448,965 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001102890 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955989 (Get FASTA)   NCBI Sequence Viewer  
  XP_063136370 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000069686
  ENSRNOP00000069686.1
Reference Protein Sequences
RefSeq Acc Id: NP_001102890   ⟸   NM_001109420
- UniProtKB: D3ZTA4 (UniProtKB/TrEMBL),   A6HLS5 (UniProtKB/TrEMBL),   A6HLS4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069686   ⟸   ENSRNOT00000086785
RefSeq Acc Id: XP_038955989   ⟸   XM_039100061
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063136370   ⟸   XM_063280300
- Peptide Label: isoform X2
Protein Domains
RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZTA4-F1-model_v2 AlphaFold D3ZTA4 1-413 view protein structure

Transcriptome

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

Promoters
RGD ID:13701955
Promoter ID:EPDNEW_R12479
Type:multiple initiation site
Name:Rbm41_1
Description:RNA binding motif protein 41
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_6.0X111,325,185 - 111,325,245EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590579 AgrOrtholog
BioCyc Gene G2FUF-1549 BioCyc
Ensembl Genes ENSRNOG00000057622 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000086785 ENTREZGENE
  ENSRNOT00000086785.2 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RBM41/RNPC3 UniProtKB/TrEMBL
  RRM_dom UniProtKB/TrEMBL
KEGG Report rno:680581 UniProtKB/TrEMBL
NCBI Gene 680581 ENTREZGENE
PANTHER PTHR16105 UniProtKB/TrEMBL
  RNA-BINDING PROTEIN 41 UniProtKB/TrEMBL
Pfam RRM_1 UniProtKB/TrEMBL
PhenoGen Rbm41 PhenoGen
PROSITE RRM UniProtKB/TrEMBL
RatGTEx ENSRNOG00000057622 RatGTEx
SMART RRM UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A6HLS4 ENTREZGENE, UniProtKB/TrEMBL
  A6HLS5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZTA4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Rbm41  RNA binding motif protein 41  LOC680581  similar to CG30327-PA  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC680581  similar to CG30327-PA      Symbol and Name status set to provisional 70820 PROVISIONAL