Special

MmuINT0065272 @ mm9

Intron Retention

Gene
ENSMUSG00000026193 | Fn1
Description
fibronectin 1 [Source:MGI Symbol;Acc:MGI:95566]
Coordinates
chr1:71639645-71642376:-
Coord C1 exon
chr1:71642238-71642376
Coord A exon
chr1:71639810-71642237
Coord C2 exon
chr1:71639645-71639809
Length
2428 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
TCTCCTTCTTTTCTTCATAGTCA
3' ss Score
9.41
Exon sequences
Seq C1 exon
TTCCAAGTTCCTGGAACTTCTACCAGTGCGACTCTGACTGGCCTTACCAGAGGGGTCACCTACAACATCATAGTGGAGGCACTGCAGAACCAGAGGAGGCACAAGGTTCGGGAAGAGGTTGTGACTGTGGGCAACGCTG
Seq A exon
GTAGGTACACTGCTGGCCTGTTGAGGCACACGCTTCTTGCTGGATCAGCCCAGAGAAGACTTGGTCTGTCGTTCTTTGTTGGCTTTAAACTTAGGAAAATGAGATTGCACAACAGTCAGAGATGTCCCCTTATGTAACCCATATGTTCACCAACACATATTGACAGGATGCCAGGCCTGGGAGGGACATGAATATTATTTACTCTAATACATTTTTCCCCTCCTGTTGAGGATCCAGTTGACAGAGGCAATGGTTTTTTGTACCTTTTACTATTCTCTCATCCCATACTGTGGTCCACTTAAGCGTTCCTAACCCGAACCGAACACCTATAAACAGTCCTCCTTGGCAATCTTAAGTGATGACTTAGGTTTTGTACCTAATGTAAAATGTTACCAATATTGCCCTTTGCTTTCCTAAGAGCTTCCCATTCCAAATTTCAACTTTATATACTTCTTTGTTTTCTTCTTCTTTAGATTTACGTATTTTAATGTTATGTGTACGGGTGTTTTGCCTGCATGTATGTGTGCAACATGCATTCAGCACCCATGGAGGCCAGAAGAGGACACCGGGTCCTCTGGAACTGGACTTATAGAGGGTTGTTAGTGACTATGTGGGTGCTAGAACCTATGTAATGTCCTGTGGAAGAGGAGCCAGTGACATAACTCCTGAGCCATCTCTCCAGCCCCTTTATATGTGTCTTAATACATAAATTATATATGTCATGTTATATACATGCAAGCTCTTAAAGGTTAAATGGCCATCATACAAACGTAATAAAGATGAAACGACCCCCATGCAGCCTTTTAATAAAGGTTAAATGACCAGCATGCAACATCTTAATAAAGGTTAAATAAATTTAATCCTGAAAATTTTTGATAAAGGTTGAATGACCCTGACTCTGAGAAGCCTTTTGAAGCCAGTGATGTGTCATTTGGCTTAAGTTGCAATAGCTAAAGATTCACCAAGGAGCATGAGTTAAGGGCTAACTGAGACTGGATCCCGAGTCCTCTTACCCTGGAAGGGCTAACTCCCACTTTTTCCAGGGAGCAGGACTTCTGGGTAGGACCACTGCCTTCTTTTCAGCCTTCTTCCTCTTAGCGAAGACTGCTATTATTTGACTCTTCAGTTAAGCAGTTGCATGTCTGGCAATGCAGAAGTGGGCAGATCTTCTGTGTTCCATCCACAGTAATTAGCATTTGCCTTTTGTGGTTTCACTAGTAAAATGCCACTTGAAAGGGATTTTTTTCAAAAGCATAGGGGTTTTGTGGTTTTCCACATCATTTTCTTGAAGGTGTGTGTGTGGTGTGTTTCAGACAGTCCTACTGTATTGTATGCTGTTTGTATATAGTGTGCTAGACTGAACTGCTATGTAGCCCAGGCTCCTAATGTTAGGGCAGACCTCCTAGATATTTTAAAATAGTGAACCCCCATGAGAGTTTTAGCCCCTTTGTTTTCTTTCCGACTCCTGTCTTTACCAGGTCCTCTTGGTTTCAAAACATTTTGGATAGACTTTTTAGTTCTTCCAGAATGATGGCTTTTGAAATATTAGGCATTTCAAATATTGATTTCATTTGCACTTTTGATTTTTACACTATTAAAAGAAGCTATCCACAAGTAGGATTTTTTTTTTCCTGAGACAGGGTTTCTCTGTATATAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACTAGGCTGGCTTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTACGGGGATGAAATCTTGGGAAACCCACTGCAGCTTTTCTACTTATTCCTAACTGCACGGTGGTGATTTCTCTTACTTGAAAATCAGGTCTTATCTAGTTTTACAGTAACCATAAGCATCTAGGTTTTCAAACTATTTAGCAAAAGAAAAGCTACAATGTAAGTAAAGATTGTGTTATAATGCTATATAAAGATGCTAAGACATTGACTACAGCAAAGACGTATCTAACAATAATTGTTAATTATTGAGTAACAGTAGTTAGTAAGTCATCTCTGCATAGTGATACTGGTCCAGAGCTTTGATTCCTCAGTTTCATGTAGCCTTTACAAGATCCAAAAAAGTGGGGCTAGTTATATTATTATCCCGTAATAGATGAGAGAAGAGAGACAGACAAATGTTAATTGGCTCCATGTACTCAGGTGTCTTGGGGAAGCACCACTGCCCATATTCTCAGCTAGTTAAAATGCCTGACGATCTGCTTCATGTCATGAGAAACAGAAGACGGGAATGAAGGAAGACGTCCTTTGACCCTGCTGTGACAAGTGCCTACTGACTGCATCAAAGTGTTGCCGATGAGAACGTCTGTGTTGTTAGTGCTGATTAGGTCACAATATACAGTATGGCCGTTTCCCCATCAATAACCGTCAATAAAATGTCTTCTCCTTTTTTTCCTTTCTCCTTCTTTTCTTCATAG
Seq C2 exon
TCAGCGAAGGCCTGAACCAGCCTACAGATGACTCATGCTTTGACCCTTACACGGTTTCCCATTACGCCATTGGAGAGGAGTGGGAGCGGTTGTCTGACGCTGGCTTTAAGCTCACATGCCAGTGCTTGGGCTTTGGCAGTGGTCATTTCAGATGCGATTCATCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026193-Fn1:NM_010233:41
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.319 A=NA C2=0.036
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0004116=fn3=PD(45.8=70.2)

							
A:
NA

							
C2:
PF0003913=fn1=WD(100=71.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000054499





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000084509, ENSMUSP00000095306
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:215368028-215370293 
ALTERNATIVE
HsaINT0065288
(FN1)
Human
(hg19)
chr2:216232751-216235016 
ALTERNATIVE
HsaINT0065288
(FN1)
Rat
(rn6)
chr9:78907819-78910593 
LOW PSI
RnoINT0061802
(Fn1)
Cow
(bosTau6)
chr2:103888015-103890734 
LOW PSI
BtaINT0063316
(FN1)
Chicken
(galGal4)
chr7:4336698-4338161 
LOW PSI
GgaINT0046549
(fn1)
Chicken
(galGal3)
chr7:4365103-4366566 
LOW PSI
GgaINT0046549
(FN1)
Zebrafish
(danRer10)
chr1:4811445-4811526 
LOW PSI
DreINT0069208
(fn1b)
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"