Special

MmuINT0023990 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr1:164621272-164622755:-
Coord C1 exon
chr1:164622504-164622755
Coord A exon
chr1:164621365-164622503
Coord C2 exon
chr1:164621272-164621364
Length
1139 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TTTCTTTTACTCCTCCACAGGAG
3' ss Score
10.52
Exon sequences
Seq C1 exon
CTTCCAGACTTGAGTCTGGTAGAAAACAAAGAACATAAACCTGGTCCCATTGGAAAGGAACGATCATTAAAAAATAGAAAAGTGAAAGATGCCCAGCAGGTCGAGCCAGAAGGACAAGAGAAACCCAGCCCAGCTGTGGTCAGAAGCACTGATCCTGAAACAGCAAAAGAAACCAAAGCAGTCTCCGAAATGTCTGCTGAAATTGGGGCGATGATCTCAGTCTCCTCTGCAGAGTATGGCTCTGATGCAAAG
Seq A exon
GTAAGTACACACTGACTGCTTATTTATGAGTGACAGGAACATTAATCATGGACTTCTTATGCGGAGCATTTGATTATAATGGTGGTTGTATCGAGCCCTTTTTGGTGACTTTTGTTGTTGTTTGGTTTTGGGTTTTTGAGCCAAGATGTAGCCCCAGCTGGCTGGCTGCCGTGGACCTCTCTCTCTGTAGACCAGGCTGGTCTCTAACTCAGATCCACCTGCCTCCGCCTCCTGAGGGCTGGGGTTACCACCACCTGGCATACAGCAAACTTACTTTGTGATGTTCTATCATACAATGTAAATGTCTCTGCAAAAGGTTACATTTTTACAGAAGTATATCTGTATTTTGCTGAATGGCTTAAATAGAAAACTGTAAAAGATCAGAATTGTCTCCCTTAAGTTTGTAAGCATTCAAAGTTGTCTTTGTCTGGTAGAACTTTATTTTGCCTTCTACTATAATTCAAACTTAAGGTGAGACACACTTGGAACACATCACTGTTTCTGAGGTTGAACACTAAAAGTATTGACTTGTTTTTGGTTGCTACATTGAACGAAAGATATGTATCTTTTAAAATACAGTCAGCTCCCTTATATCTGTGAGTTCAGGATCCATGAATTCAAATCTGGATAAAAAATATTCTCTCTCAAAAATTGGAGGTGTTTTGTTTTGGGTTTGTCTTCATTAAACTATAACATCCAGTGGCAGAACATTTCACTGTATTCCAGGTTATTAGTTATTTAGAGAAAATGCCATAAACCTAAGCATCTGCATCTCTGCAGGCCCGGTATGTAACAAGGTGCGCCTCGAAGGCACGTTCTGTTAGGTGACTAGAGGTAGATAGACACTTGTAGTCATTAGGGGACATAACTCATAGAAAGAAATATTTAGTTTTGCTGATAGCCTTCTACCTCATGCTATGAAAATAGATTTTAAATATGTGTAAAAGTCTAGCAGCAACTGAGATGTTGTCTCTTGAAGGCAGGCGGGTTGATGCTCTTTCAGCCTACTGTTAGTTGGTGGATTCAAGTTTTAGGGCATAGTGGTTTATTATCTCTCTCCTTCTAAAATAGCTTTACTTCTATTAGACTGTCAAAAATGGCCGATAAATTCAGCTTTGTTTTCTTTTACTCCTCCACAG
Seq C2 exon
GAGTCTGTAACAGACTACACCACACCTTCCTCTTCTCTGCCTAACACTGTGGCTACTAATAATGCAAAGATGGAGGATACTTTAGTTAATAAT
VastDB Features
Vast-tools module Information
Secondary ID
-Bat2l2:NM_001081290:22
Average complexity
IR-S
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:
ENSMUSP00000028016





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028016f5784A, ENSMUSP00000038401, ENSMUSP00000038999
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:171566844-171568246 
LOW PSI
HsaINT0016712
(PRRC2C)
Human
(hg19)
chr1:171535983-171537385 
LOW PSI
HsaINT0016712
Rat
(rn6)
chr13:80562415-80562665 
Cow
(bosTau6)
chr16:39910615-39912209 
LOW PSI
BtaINT0118641
(PRRC2C)
Chicken
(galGal4)
chr8:4735251-4740301 
Chicken
(galGal3)
chr8:4868553-4877474 
LOW PSI
GgaINT0035915
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GACTTGAGTCTGGTAGAAAACAAAGA

				
R: 
TAACTAAAGTATCCTCCATCTTTGCA

				
Band lengths: 
334-1473

			

		

	





	
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






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