Special

MmuINT0023950 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr2:32068407-32071753:+
Coord C1 exon
chr2:32068407-32070467
Coord A exon
chr2:32070468-32071565
Coord C2 exon
chr2:32071566-32071753
Length
1098 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACG
5' ss Score
10.19
3' ss Seq
GACTCTTCCTTCCTTTGCAGGTC
3' ss Score
13.01
Exon sequences
Seq C1 exon
GAATGAAAGGTCTTACTGTGCCTCCCCCGGAAGGCCAGGGGGCATAAGTGCCCAGCGCGATCTCTTTGAGGAGAGAGGGGAGGAGTTCTTGAGTGCTTTTGACAAGAAGGCCCAAGCAGACTTTGACAGCTGTATCTCTTCTCAAAGAATAGGCCAGGAGCTTTTATTTCCACCCCAGGAAAATGTTCAGGAGGTGGGTGCTCCTGGGGGTTGTACCCCAAACCTCAGGTGTTCCCCATTGGAGCCTGACTTTGTCCCAGCTGAGAAAAAGCCAGAGTATGGCAGCTGGGATGTTGGCCACCAGCCAAAGGCCGCCGACACAGCCAACGGTGTCGAGCTGGAGGCTCCCCGACAGGAGCCTTCCTTTCATGTTTCCTCTTGGGAGAAGGAAGGGAGCCCCAAGAAACAGCCAAACCCGGAGCCTGAGTGGACACCTGAGCCCCGGAGCTCCAGCGGCCAGCACCAGGAGCAGCCGGGCAGGACCCGGAGGTCAGGACCCATCAAGAAACCAGTTCTTAAGGCCCTGAAGGTAGAAGAGAAGGAGAAGGCCCTGGAGAGAGGCAGGCAGGGGCTTAGAGAGGAGAGCTCACAGCGGGCCCCAGAGAAAGAACCCGTGGGCAGGGCCGAGGAGGACGAAGAGAACAACCCTGCCCTAGCCAATGCCTCCTCCGCCCTGGAGGACAAGGCTGCCTCCCGGGCTGGTTTTGCCCACGAGGCTAGCAAGCTGGATGAAGATGAAAAGGCAGATAAGACCTGGGAGAGCAGGCCCTCAAGGGAGGCCAGTGACATTCCCCCAACCAAGAGAAACAACTGGATCTTCATTGATGAGGAACAGGCCTTTGGGGGACGGGGCCAGGCCCGTAGCCGTGGCCGCGGCTTCAGAGAGTTCACCTTCCGGGGCGGCCGGCCTGCAGGCAGCAGCACAAGTGGTCTTTGTGGCACGGGTGTCCTTGGGTCTCGTGGCATGTACAGTAGTGGCCAGCGCAGTAACCGAGGCAGGGGCCTGCGTGACTTCCCCCCACCAGAAGACTGCCCCAGAGCCAAGCCAAGGCGTCGCATTGCCAGCGAGACTCACAGCGAGGGCTCTGAGTATGAAGAGCTGCCCAAGAGGCGCCGGCAGCGGGGCTCTGAGCATAGCCACGAGGGCATGCTCACGGAGAGGGACGAGGGTGCCCTGAAGGACTCATGGCGCTCCAACAGAACTTACACCGAGGACCAGGGCGGTATAGACACCCGCAGCCGGGGATCCCGGACATGCGGGAGAGCCCTCCCACCCCGCCTGAGCAACTGCAGCTATGGCCGCAGAACCTTTGTTGCCAAAGAACCTCCCCACTGGCAGAGCAGGAGCCCAGGCAGCTCCTGGCAGGAATATGGCTCCTCTGACCCGTGTGGCCCACGGCGAGGCACCGACAGAGACTACATACCAGACTCCTACCGACAATCTGACACATTTGGAAGCAGGCTTTTTGAGGACAGCCGCACGGAGGACAAGAGGTCCTTTTTCCAAGATGACCATGGGGCAGATTCTGAAAATGCAGAAAACAGGCCCTTCCGTAGGAGGCGGCCCCCACGCCAAGACAAGCCCCCTCGCTTCCGGCGCCTCCGTCAAGAGCGGGAGTCCCTGGGCCTGTGGGGACCTGAGGAGGAGTCCCATCTGCTGGCAAGCCAGTGGCCAGGCCGGTCCAAACTCTGTCCTGGGGACAAGAGTGGTCCTGGAGGTCACAGATCCCCAGAGCTTTCCTACCAGAATTCCTCTGATCATGCCAACGAGGAGTGGGAGACCGCCTCCGAGAGTAGTGACTTCAGCGAGCGTAGGGAGCGGCGAGAAGGCCTCGTGGCTGAACCCGAAGCGCAAGGGGATGGTGGCCTCTCTGGGTCCAGTTTGGGTGAAAAGAAGGAGCTGGCCAAGAGGAGCTTCTCCAGCCAGAGGCCCCTGGCCGACAGACAGAGCCGCAAGCTGGAGCCGGGAGGGTTTGGGGAGAAGCCTGTTAGGCCAGGTGGGGGTGAGCCTTCCCCCCGCTGCGAGAGCCAGCAGAGCGGGACGCCTCTGAAAGTCAAAAG
Seq A exon
GTAACGCGTCAGCACCATCGCGGGTCCTTTGTCGTTGTCCTGTTCGCAACAGCATCAAGTCCATGCATGCACGCCCTGCCAAGCCAGGCGGCCCCGGCCGCTGTGTGTGAGCATCTCCATCACGTGCTCCTGCATTGCTTGTCTGCTTCTCCATGGTGTGTCATTGTTGATGTTGTTGTTGTGGCTTGATCAACTAGACCCAGAGTTCCCCATGCCCTACTCCCCGGAGGCCTTCTTGTGACTGCTGTTCTAGCCCGTGTTCCCAGAGTCCAACCTCCGGATATATCCTCAGCTCTGCCCTGACGGCTGTTGCCTGTGTGTGGTGCCCGACAAGCTCTGCAGTCTACCCGCTTGGTACTGCTGCAGCTGGTCAGAAGGCAACACTCACTTTTGGTCATGTGGAGAAAGCTCTTGCCCCTAGTGGCCCTGCTTCCCTCGTGCTGCCTGGACATGGCTGGAGCCACCAGGAACAGAAGGGAGCAGCCCGCTCTCAGCCAGAGCCTGCTTTTCTAGAAGCTGAAGCTTATGGGGTGGCCCATGGCCCAGGCTGCCTGTAGGGAGAATGTGGTCCTGCTGCCCAATCAGCGCCTCAGGTTGAGATGTCTGGGGTGCAGAGGTTTTACCCCTCCTGTCCTTAGAATTCAGAGTTCACAACTCACGTGTACATACCCCAAAGAAGTTGACTCAGGAGAATATCTGTTAAGTCTCGGTGTGACTATACTGCAGCCCCAACAAGGCATCATGAATGAACTCAAGAGCCCTGCAGTGAGATAGCCTGTGCTGCTCTGGTCTGTGGGCCTCTCTTGGGTGCCTCCACCCGGCCTCTTCTCGGCACTGCAGTCTGTGGAAGCAGCATACAGTGGGAGGGAAGAGTACTGTGGAGAGGGTACTCCAGCAGCCTTCACCCTGCCGCAGAACAGGACCAGCACGGGGCTCGCACTGTGGGCAGGCTCTTGTGACCCTTGATGGCTCAGTCGCAGGAACCGGAACTAGATAGCTGCTGTGTCTGTGTGTGGGCCTCGTGCATTCAGATCCTCCTGCCCCTCTTTCCTAGCCTTTGAGTAGTGGAGCGTTCATGGACTCTTCCTTCCTTTGCAG
Seq C2 exon
GTCTCCAGATGAGGCCTTGCCTGGAGGCCTTGGCAGCCATTCACCCTATGCCTTGGAGAGAACCACTCACGCCAGCTCTGACGGTCCTGAAACCCCCAGTAAGAAATCAGAGAGAGAGGTTTCTTTGCCTACCCAGAGGGCTAGTGAGCAGGAAGAGGCCCGGAAGCAGTTTGACCTGGGCTATGGAA
VastDB Features
Vast-tools module Information
Secondary ID
-Bat2l:NM_001159634:16
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NA

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000064892f6238A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000064892, ENSMUSP00000114656, ENSMUSP00000121664
  



Associated events






Conservation


Human
(hg38)
chr9:131476536-131477743 
HsaINT0016673
(PRRC2B)
Human
(hg19)
chr9:134351923-134353130 
ALTERNATIVE
HsaINT0016674
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr11:101627752-101629026 
LOW PSI
BtaINT0118604
(PRRC2B)
Chicken
(galGal4)
chr17:6202330-6203150 
LOW PSI
GgaINT1022705
(PRRC2B)
Chicken
(galGal3)
chr17:6829273-6830093 
GgaINT0123924
(PRRC2B)
Zebrafish
(danRer10)
chr5:71249966-71250171 
LOW PSI
DreINT0017300
(PRRC2B)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GAGTAGTGACTTCAGCGAGCG

				
R: 
GCGTGAGTGGTTCTCTCCAAG

				
Band lengths: 
342-1440

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • 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"