Special

MmuINT0043178 @ mm9

Intron Retention

Gene
ENSMUSG00000032515 | Csrnp1
Description
cysteine-serine-rich nuclear protein 1 [Source:MGI Symbol;Acc:MGI:2387989]
Coordinates
chr9:119883272-119886363:-
Coord C1 exon
chr9:119886120-119886363
Coord A exon
chr9:119883532-119886119
Coord C2 exon
chr9:119883272-119883531
Length
2588 bp
Sequences
Splice sites
5' ss Seq
CTCGTGAGT
5' ss Score
8.41
3' ss Seq
CCTTCTCTTTTCCCTTTCAGCCC
3' ss Score
12.05
Exon sequences
Seq C1 exon
GCGTCTGTCCTCGGCTGTTGGAACCCCCTACATTCCACCATGACTGGGCTACTGAAGAGGAAGTTTGACCAGCTGGAAGAGGACGACTCCAGTTCCTCCTCCTCCTCATCGTTCTCTAGCCGGCTCTCTCTCTCCTCCTTCCCCGCCTCTTCTGCCTCCCCTGCCTGGAACTCTGATGAGGAGGGACCAGGTGGTCAGGCACCCCAGTCTGATCAGGACTCCTGTGGCCTCCAGAGTTTCACTC
Seq A exon
GTGAGTCTCCCATTCGGCTCCCCCCAACCCTCCCCCTTCTTCCTTCCCTAAAACTGAAATTGGCGTTTTTGGCCTCGGTAGCCCCCTCAGGGTGCCTCCTTCTGTGAAGTCGTGTGACTGCTCCACTCTGCAGAGACACCTTGACTTCCTGTTGACCGTGGGGGTTGTGCTGTTGGAGTCCGAGACTTTGCTTGAGTGGCTCTGGCTCTGGGGCCTTAGAGGGGTGTTGCGGCTCTGTTTCCCCGGCACACCCTACCCCTTCCAGGAACACCACTGGGGCTCATCCCTCTGCTTCCACCCCCCCCCCTGCACTAGGCCTGCTAAGCCTCTTCCCTCTCCCTCCATTTTAGCTTCTTTCTGAATGTCCCCAAAAGGGTTTTTCCAGAATAGTTTTCTTCTCTTCCTTTTTTTGAGAGCACACTCTCATATAATCCAGGTTGCCTTCCAGCTGTGTGGCATCTGCCTCCCAAGTACAGGGATTCGGGATGCACGCCACCATGGCTGACTTCCTGGTTATCTTTCTCTCTTTTTTTTTCTTTCTTTTTTTAAAGACTTATTTATTTTATAATATGTGAGTACACGCTCACTGTCTTTAGACACACCAGAAGAGGGCATCAGATCCATTTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAATTCAGGACCTCTGGAGGAGCAGTCGGTGCTCTTAACCTCTGAGCCATCTCGCCAGCCCCCTCCCTGGTTATCTTTCAAGTTTGTATAATTTTGATTTTAAACTGAAAGATGGTCTTGATGGTTTTTTTTTTTTTTTTTTTTTTTTTTTGGGTTTTTTCAAGACAAGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGTGTGTGCCACTATTGCCCAGCGATAGTCCATTTTTTAAAAAAATTATTTCTTTTTATTTTTGAGATTATAATTACATCATTTCCCCTATCTTCCCCTCCCTCCAAATCTTCCCACATATCCGTCCTTATCCTCTTTCAAATTCATGGTCTCTTTTTTTTTTTTTAATTATTGTTACATAAGTCTATACAGCTATATTCCTACATATATAACTCCAGCCTGCTTTGTTTTTATAATGTAAAGGCAACCTTTGATTTTCAGCATGCTCTTTCTCCTTCAAGAACCATTTTAGACACTTTTCCCCTACAAGGGGAATGTTTATAAACACAGGATTACGTCTCCCTATGAAGTTTTGAAACCATAGTTGTTCCTTCCATGTCTCCTATACAACATACCTGTGTGTTGCATATTTTTTAAAAAAGTATGATTTTTAATGCCTGGAATACTAACAGGAAATTTCTTAGAAGGAATTTTCTCAGGTAGTTGAGTACAAAGTTAATATGTTAACTTGAAGTCACTTGGCAAACATATAATCCCAGAACCGGGGAGGCAGGAGGGCTGGGGTTCAATGTCGCTTGCTGTTGAACCAGTCCTAGCCAGCTTGGGATAAATGATGGTGTATGCCTTTAATTCCAGTTCTTGAGAGACAAAGCCTGGTGGATCAAGACCAACCTGGGCTACGTATCAAGTCCTCGGACAGTCAGTGTTACATAGTGAGACCTTGTCTCAAGAAAACATAAACAAGGGCTAGAAGGATGGCACAGTAGTTAAGAGAATCTTGCTCTTGCAGAGGACCCAAGTGTGGTCCTTAGCACCCACATCAGATGGCTCACCACCACCTGTAGCTCCTAGCACTAGGGATCTGGCGCTTTCTGAACTTCAAAGGCACCCACACCCAAGTGGCATACACTCACACATGCACTTATTAAAAATAAGTAAGTTTGAATTGGGCAGTGGTGGCGCATGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAATGAGTTTCAGGACAGCCAGGGCTACACAGAGAAACTCTGTCTCAGAAAACCGAAAGAGACAGACAGACACACTTTCTGGGTCTGTTTCAGAAGACTTAAACTATAAAGGAAAAGACCAATGACACAAATATATATTTTTAATTTATGTGCATGAGTATTTTGCCTGTGGATATATGTCTATGTACCATGAGCTTGTTATGCCTGAGGAGGCCAGAAGAGGGCGTTAGAGCTTCTGAAACTGAGTTTCTTGGCTGCGACCTCTCCTGTGGGTGCCAGGGCTCTTAACTGCTGAGCCATTTCCCCAGTTCTTTGATATATGTTTAAACAGGGGATTATATTATTACATGTAAAGAATAAGAATTACAGAAAATTGTACAAAGGATTTATAAATCCGTGGTAAGGGTGGCAAGACGCTTCATCTTTGCGGGTTCATTTGTGCTGAGAAATGACAGTTAAGCTGGTGTTGGGTTGGGGGTGGTATTGTTCTCCAGATCCAGCCAGGCCTGGCTTTTAAGTTCAGATCCAAGGTGGGTGGAGAAAGAGAAGGGGTTGGAATCTTTCTAGAGATTATACCACATCGAGGGAAGCTCAATCCCTTCTCTTTTCCCTTTCAG
Seq C2 exon
CCCCGTCCATCCTGAAGCGGGCTCCTCGGGAGCGTCCAGGTCACGTGGCCTTTAACGGCATCACCGTCTACTATTTCCCACGGTGCCAGGGATTCACCAGTGTGCCCAGCCGTGGTGGCTGTACCCTGGGCATGGCTTCTCGGCACAGCACCTGCCGCCTTTTCTCCTTAGCTGAGTTTACACAGGAGCAGGTCCGGGCTCGGCGTGAGAAGCTCCGCCGCCGTTTAAAGGAGGAGAAGCTGGAGATGCTGAGGTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032515-Csrnp1:NM_153287:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.652 A=NA C2=0.218
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000035101





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr3:39145257-39146477 
ALTERNATIVE
HsaINT0042477
(CSRNP1)
Human
(hg19)
chr3:39186748-39187968 
LOW PSI
HsaINT0042477
(CSRNP1)
Rat
(rn6)
chr8:128663049-128665609 
ALTERNATIVE
RnoINT0042831
(Csrnp1)
Cow
(bosTau6)
chr22:12522681-12526042 
ALTERNATIVE
BtaINT0044802
(CSRNP1)
Chicken
(galGal4)
chr2:5229940-5232203 
ALTERNATIVE
GgaINT0097826
(CSRNP1)
Chicken
(galGal3)
chr2:5162516-5164779 
LOW PSI
GgaINT0097826
(CSRNP1)
Zebrafish
(danRer10)
chr24:19564966-19567010 
LOW PSI
DreINT0052812
(csrnp1b)
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"