Special

MmuINT0132939 @ mm9

Intron Retention

Gene
ENSMUSG00000026970 | Rbms1
Description
RNA binding motif, single stranded interacting protein 1 [Source:MGI Symbol;Acc:MGI:1861774]
Coordinates
chr2:60596861-60600203:-
Coord C1 exon
chr2:60600110-60600203
Coord A exon
chr2:60596912-60600109
Coord C2 exon
chr2:60596861-60596911
Length
3198 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTGT
5' ss Score
7.44
3' ss Seq
TGAAATCCTCCGTTTTCTAGGTG
3' ss Score
10.02
Exon sequences
Seq C1 exon
ATTTTATCCTTCACCATACAGTATTGCCACAAACCGAATGATCACTCAAACTTCTCTTACACCCTATATTGCATCTCCTGTATCTGCCTACCAG
Seq A exon
GTTTGTACCTCAGGACTCGTCAGCAGTGCACCATGCATCTCTGCTGCATTTTTATGTGTCTTCAAATTCTGAACAGTTTTTAAATGAAATCTAAGTCAAATTGGATGCAGCTTGGATACCTAGTTTGGAATAAGCTGCCTTTTGTTTGGCATAGCAGTTTGCTTTTCCTTGTAGGAAAGCGTAAAGCCAGGGTAGTGGTTGGAATCATCACATGGTTCTAGGAATCGGAATAAACCCTCGTGCTTTCTCCATCCTGTGCCCCAGAAATTGAATCTTTATGAGAGTCACAAAATGGAGAGTGAATTTGGGCTTCTGTCTTCATTTCTTCACTAGCAGGAAGAGATAAAGGGAACACAGAGATTGTCTCTCTTAGGTGACATGGGCTGATACAGTTGAGATTTGAGGTCCTTCCCTGATCAAGAAGCAAGAGGTCATTAACTCCTCTTCAATTACTTTGTGAGAAGGCTTTACCTTCAGCCTGGAGTGACCCCTCATTAAGCTCCTTGTCCAGCACTGATCTGATAGTATTACAGGGCTAGCAGGGCCGGTGCGCCTTTCTCTTCCTGTAGCAGAGTCTTCCGCACAGCTCTATATGGCCTGGGCACTGACGTTAGCACTGTCACTGAGTTCAGTTACTGACCTGCAAGAGAGTTCTCTTCTGTTGACTGCTGGGGTCTTGTGTGACTAAACTCTGGGGTATTCTTGTTTTTAAAACTGAATTAGATGTTGTAGTCCTGACATCAGGGGTTAGGGGACTACAGCATCTGATCTATGTTGTTTGATAGCAACAAGCCTCGGGTTCCTCTTCTTTAAAATGGGGATAATAATGGCTTCTACTTTATAAACTAGAGAGAGTTCTGAGCACCTAACGAAAATAAAAAGAGCTCCACCAAGTACTGACATATCACTAATAGTAAGCATGCGCTAGCAGCAGCAGTGTTACATGTTAGTTACCCTTTTCCAATAATGGCCAAGGTAAGACAATGTCAAAGTTGGCTCTGCGTAAGTTGTGAAAGTAACACTGAAAAATAGAAGGAAGTGTGTGCTGAAAGCAAAGTCTCACCGCATGGCCTCCACCTTCAGACATCTCTGTCTCTCTGACTCTCTCCCTCTCCCTCTCCCCCTCCCCCTCCCCCTCCCCCTCTCCCTCTACCTCCTCCAGCCTCTATTCCTTTCCTTTCCTTTCTTCTCCCTGAGTTGCTACCTGACTCTGAAGTGTCAGTCTTCTGGACAAACTATTTATGTCTCTTCAGCTGTTGGGGAGTTGAGATTTTTGTCTTTTTCCCTGTTTCTCAATAAGAGCGCATGGATAATACAGTACATTTCCCCTCATAACCAGCATATATAGCTGATATTAGAGTCTTTGATGACCTGAAAATGACACTTTCTGTATCATTAAAAATAATGGCAGGTATAAGCTCCCTCTTAAGCAAATGAAGACTGTATTACTGTGTCGCTATAGATACGCCCGCTCCTAATCCATCTGTCTACCACTTACTTTTCTTCTTTTAAGCTGTTTGCCTGTCAACCATTTTATAGAGTAAACAGTCAGGAGGCCAGCATTGGAAACCAACTGGACATGGCTAACTGCAGACAGCCTGTCATTTCAAGGCTTCGTTTCCTCCTTGGGGAATTCTGTGGTTTTTGTAAGACCCATGTGAAATTTACTCCATTTACCTGACAGAGGCAAAACCTCTCTGTCAGTGCTGAGCAGAGGTCAGGGCATGCGCCCCAAGTAGTCTGAGGTCCCTTTTAGTTGTGTGCAAAAAATGTTATCTATGTATGGTTAGTTTGGGATGGGGGCTCTATTTCTTTCAGGTTTTCAAAGAAGCAACAATAAGAAGTTAATAGATTATTATTCCCATTTTATAACTAGGGAACATTGAGGAACAGCAAGTGACAGTGGCTACTTTGCTGCTGAAATATAAACATGGGATTAGATGTCATAGCTCCCTAACCCTATAATACTATAAGTTCATAGGCAATTATGGCCACAGAAGCATACAGAAGTGGGGGCATCTGGCCCAGATTGGGGTTTTCAGGGAGCCGCGTGCCTCTCGTGATGTGTCCATAAGGGCCTACACTCATTGGAGTTGGCCTTCTCCACTAAACCACCATATGCTTATGCAGTTGGATTGAGAAAGAGGCATCTGCGAGAACCCACCAGTACCCCAGTGGGGAAAGGCTGCAGTCCAGATAACTGAAATGTTAACAAGGCAGAAGCACTTAACTTTGGTCTGCCTTAGGTGGCAAAGGAAACCAGAGAGAACAAGTATCGGGGCTCTGCTATCAAGGTAAATCACACTACATTCTTTCCCCATGACTCTTCCCCGTATTCTCTCTGTAGAATCTCTGAAGTTTAACACTCAGGGACAGGATACAGGAGGGTGCTGTCTTATCAGCACTGGAAATGGAAATGGACCTTAAGATCCCATAGACCTTGAAAAACCATGGGCATCAAGATGCAGACTCAACTCCTCCGTGGCAGGAGGGGCATTTCTTTCCTGCCACAGAGCCCGACCCTCACATCGTACTTGTCAGTTCAGAGGGTTACCGTATGGATGCCCTTTTAACTTAACCGTTAACCTCGAGATCTTCTACCCCCCGCCCCCCATTTGATATCCTAGGTCTGCATTTCAGACATTCTTTTTCTCCCTACCTAGAAATTGTTGAAGACTACACAGAATTGCTAATCTTACTTTCCTGATTATCAGAGATTGTATTTGGTTATGCTTAATAAATAGTAGAATAGCCTGTGTGCACTGAGAGGGCTAGTGTCTAACTAAGTTCTACGATTAATCCTCATCCATCAGTATTCCTAAAACGTAGCCCATAGCTTGATTATAACACTTTTCACTAATTTGGGTTGTTTACATGTTTATTTCTTTTGCTTAGACAGTCACTTTCTCAAGGGTGAGGCCCATCCGTGCCTTACCCTCATTGCTCCCTGGTGCCTAATGTTCAGTAAATACGCACCTAGTGGGCAAACTGACATTGGTTCCAAATGATTGCTTCATCTCGTTTAGACTGACCAGTTTGTCAAGAGTTCTAACTGCCTTAACCTTTGCAATTGATAGCATTGTCTCCTTATCTTCCTTCTGTAGATTTTTTTTAACACGATTAAAAAAGAATTCTAGAGAGTTAAGGCTCTTTTGGCAGTAGACATCAATGTTTCTTTTGAAATCCTCCGTTTTCTAG
Seq C2 exon
GTGCAGAGCCCCTCTTGGATGCAGCCTCAGCCGTACATTCTGCAGCATCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026970-Rbms1:NM_020296:9
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.092
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF072716=Cytadhesin_P30=FE(23.7=100)

							
A:
NA

							
C2:
PF072716=Cytadhesin_P30=FE(12.2=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028347





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000108128, ENSMUSP00000108129, ENSMUSP00000131306
          









    
Other Skipping Isoforms:
ENSMUSP00000129560, ENSMUSP00000130047
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr2:160281365-160284774 
ALTERNATIVE
HsaINT0138664
(RBMS1)
Human
(hg19)
chr2:161137876-161141285 
ALTERNATIVE
HsaINT0138664
(RBMS1)
Rat
(rn6)
chr3:46809635-46812776 
ALTERNATIVE
RnoINT0125319
(Rbms1)
Cow
(bosTau6)
chr2:36166047-36169408 
ALTERNATIVE
BtaINT0123461
(RBMS1)
Chicken
(galGal4)
chr7:21255307-21257498 
ALTERNATIVE
GgaINT0046221
(RBMS1)
Chicken
(galGal3)
chr7:23343881-23346072 
LOW PSI
GgaINT0046221
(O73664_CHICK)
Zebrafish
(danRer10)
chr23:25830901-25832620 
LOW PSI
DreINT0125513
(rbms2b)
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"