Special

MmuINT0132829 @ mm9

Intron Retention

Gene
ENSMUSG00000036249 | Rbm43
Description
RNA binding motif protein 43 [Source:MGI Symbol;Acc:MGI:1918934]
Coordinates
chr2:51782201-51785369:-
Coord C1 exon
chr2:51785180-51785369
Coord A exon
chr2:51782281-51785179
Coord C2 exon
chr2:51782201-51782280
Length
2899 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACC
5' ss Score
9.24
3' ss Seq
TGATGCTAATGTTTCCCTAGTTG
3' ss Score
6.62
Exon sequences
Seq C1 exon
GCATCAGCGTGGAAGGTCAAAGATCCTACAGTTGCTGAGAGAACAGTTGTAGTCTCTGGACTTCCAGTTGGCCTTTTAAAGGACCAGTTAGTGAAGTGCTACTTCCAAGACGAGGGTGGACATGTGGAAGAGGTGATATATCCATCAAAATCCAAAGGAGTTGCGTATATCATCTTCAAGGAAAAGAAAG
Seq A exon
GTAACCAAGATTTTATTATCTGAGAAGTGCTTTCTCGGTGACATTAAAATTTCATATTGTTAAAATGACTGATGGGATTGGCAGCGTTTGAAGTAGCATAAAAAATTACTCTGTTCTGAGAAGTGGCCAGTCTTATGTTTGCAAAAAATATATGAAAATAGCTTATGAAAATGTGTCAGTGAGTGAAAAAAATTGAAAACTTTAAAAAGTATTTTGCATATATATATACACACACACATATATATATATATACACACACACACACACACACACATACACCTTAGGAGGCAGATATAGAACATGTGTAAAATAAAGTTGAATTATATATAATCTCCTAGATAAGACAACTATTTAGGGAAGTCTCAGGTGGCAGCAGCAATATAATCACACTCTCTGCTTCTAATCCCTCCAACTATCAAGTGAAAAGTCCTTTTTTTTTCTTTTTTTAAGATTTATTTATTTATTTTATTCATATGAGTATACTGCAGTTGTCTTCAGACACACCAGAGAGGGCATTGGATCCCATTACAGATGCTTGTGAGCCGCTAGGTGGTAGCTGGGACTTGAAACTTAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAATCACTGAGCCATCTCTCCAGGCTCTCAAGTGGAAATTCTAATAAAGAGTCTGCTTTGTTACTGGTTACATTGAACTGAGAACTATGGCCTGCACCTGAAATAGGACTGAGGTGTTCTGTCTCCCACTCCATCTTGAAACAGCCAGCTGCAGATTGGTGGCTGCAGATTGTCCTTGCTACTCCAGCCTGGAGGAGGGACAGTCTTTTTTAGGCTTAGATGCTAGAGGATAAATGCCAGAGAACATTCTCCGTGCTCTACCCCATCAGGAGCGAAAGTTCCATGCAGGTGTGTTAGGAAAAAAAAAAAGGCTCATGTTCTGTTTGGGGGTGGGGGAAGAAAAGCCATGTTCAGGTATGAGATTGTGGGAAGGGCTTGCCATCTCTTTAAAAATTCGGCAGTGGTGGTGTAAGGTGATAGTTCATGTGCTGAATATTGCTAAATACTATTCTAGATGTTGAGAATACATCCATGAGTGGAGTAGGCAGTCGTTTTGGTTTTCATGAAGTGTACATCAATGAGGTTGGGCATTTATTAGGGCAACAGATGTATAATATGTTTGCCCCTTATTTATATCTATATATGTATATTTACATTTGTTTATATGTTAACATATAAATGTTATGAAAAAGTATAGAGAATAATAAAGAGATAAAAGCAATGGGTGGTACTGCTTTAGGTAGACTGGGTCAGGAAATGTCTTTTGCTCTTTTAGCATTTTATTTGAAAAGAGTTATCTCTATTACTTTTATTTTATGGTGTGTGTATATGTGCACGCGCTTGAGTGTCTGAATATCATGTGTACAGAGGTGCTTGAGAAGCTCAGAAGAGGGAATTGGATCCTTGGAGTTGGAATTACACACGGGAGACCGTGAATCACTGGATGTGGGTGCAGAGAATGAGATTCAGGTCCTCTGGAAGAGCAGCGTGTGCTCTTTCCTGGTACACAATCTCTCCAGCTCTCTTTCTTATTTGCTTTTTGAGACGGAATTTTATCATATTGCCCAAGATGCCTAGACTGGTCTTGAACTGAGGGCCTCTGGCTTTTGTTCCGGTTAAGTTGGGATTACAAACTTGCATCACCAGATCTGGTTTGGGAACTGTGCGCGCGCGTGTATGTGTGTTGGAGATTATATCCAAGGTTTCATGTATAATAGGCATGTTGGGGATAATACCCAAGGTTTCATCTATGCAAGACATGTGCTGTACCAACTAGGTGTGTTCCCAGATATGAAACACTCTGTTTACCTAACGGTTAAGTAGAGACCAGAATGAAGCAAAAGGGGCAGGGGTGGGTGGGTGTGGTGGCTAAGGGGATAGAGAGGGATTCATGAGGATAGAGGGGAGGGGCATTTTAGGATAAATGAAGGACTGGTAAAAATTGTTAGGGTGGGGAGTGTGGTGAGGATGGAAGCGGAGGCACGTTGAGTGTGCAGAAAGAGGAAGGCAGGAATGGAATGAGTGTGGGCAAAGTAATTAATAGGTGTGCATAGCTCGTGAGCTAGGACCCACGCGTGCTGAGCAGCCTGTGGTCCAGGAGGTTTCTGGGTTGCTTGTGGTGAAGTGGGAGCTGTTGGAGGTCCTAAGTAAGGGACTGAGGAAGGGAGTTGCTCTTTCGAAACAATGTTGCAGTGTGGCGATCTATCAGTGGGTTGGGCTATAGAGAGGAATCGCAGAGCCAGTGAGTATCAAGGACACAGGTTTGAGGATGCTTGGGGGACCAGTGATGGAGAAGCAAGCTGTCCTTCATGTGACGGCTTTTAGGACAATGAAGTAGGATCAGAAGTTTGGAAGTGATACATGTAGAGATGTCTAAAGCCATAGAGGTTGAGATTAGCCACGGGTGGGTACAGTGAGGAAAGAGGCCCGAGGTCTAGATCTGCCAAGGTCGAGTGAAGAGCAGGAGATGAGGGGTTAGCAGCGAGGCAGGAGAAAAACTTCCGCAGCGTGGAATTTCTCGAAGGCAGTATTCCTCTGATGGGTGGCATGGAGGATTGACGTTAGGCTATTGCTTTTTACTCATGCATGGATTTGTGTGTGCTTAAAAGTAGAATTAGTATACATTTATGGTGAACTTTAGTGTGTTAAAGCACACAGGAAATGTTATCTGAATGTCAGGTGAAAGAGATAAATGTTGCAAAAAAACAAAAACAACAACAACAACAACAACAACAACAACAAAAGACAAAAAACCAAAACTTACTTTGCAAACAATAGAATTGAACATCTCTATTTGTAAATTAAGGTACTTACTGGTGTGTCATGCCACAAACACTTTTGATGCTAATGTTTCCCTAG
Seq C2 exon
TTGCACAAGACTTCATCAGACAAAAGAAACACCCTCCAGGCTCAGAGCCTCGGCTCACAGTCTCTCACTTCAGTGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036249-Rbm43:NM_001141981:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.222
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0007617=RRM_1=PU(76.2=75.0)

							
A:
NA

							
C2:
PF0007617=RRM_1=PD(22.2=51.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000036829





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000099828, ENSMUSP00000099829, ENSMUSP00000126129
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:151252856-151255532 
LOW PSI
HsaINT0138557
(RBM43)
Human
(hg19)
chr2:152109370-152112046 
LOW PSI
HsaINT0138557
(RBM43)
Rat
(rn6)
chr3:37437408-37440474 
ALTERNATIVE
RnoINT0125212
(Rbm43)
Cow
(bosTau6)
chr2:44968925-44969978 
LOW PSI
BtaINT0123362
(RBM43)
Chicken
(galGal4)
chr7:34601004-34601493 
LOW PSI
GgaINT0046606
(RBM43)
Chicken
(galGal3)
chr7:36726682-36727171 
LOW PSI
GgaINT0046606
(RBM43)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"