Special

MmuINT0041385 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr6:121956816-121958507:+
Coord C1 exon
chr6:121956816-121956962
Coord A exon
chr6:121956963-121958323
Coord C2 exon
chr6:121958324-121958507
Length
1361 bp
Sequences
Splice sites
5' ss Seq
CTCGTGAGT
5' ss Score
8.41
3' ss Seq
TGGATCTCCTTCCTTTCCAGGAA
3' ss Score
11.11
Exon sequences
Seq C1 exon
GGAGACAGTGTTAAGGAGGAGACACCATAAGCCCTGTCCTCCTGTCCTTTCTTACCACACCATGTGGAAGAGCAGACGGGCTCAGCTGTGTCTTTTTTCAGTTCTTCTTGCCTTCCTGCCTTCTGCTTCTTCACTCAATGGAGACTC
Seq A exon
GTGAGTACCTCCAAAGCCATCTTCGTATATTCTCTCCTCAAATCAAAAAACAATCCATTTCCCTTTACAGTCCCTTCCCCTAAAAACCTCCTTAAATTCTTTTTGCTTTATAACTAACAAATAATTGTTTATGTGTGCTTCAACTTTAGTATTGTATGATTCTGGATAATCATTTTTCCTACTCTAAAGCAATCATTGTTAGTAAACTGAGGTGTGGTGTGATTTAGAATAACTTTCCCCTTATTACTGAACAAGTAGTATCTCAAATCCCAATGGTCAGAGACATTCTCTGGTGTTGAAACTATGTAATAACTTTGAAAAGTAAGCATTTAGATTGTTAACATTCTTGATTGGAAATGTGTAGCCAGTGGTGTAACCTTGAGACAGATAAGACTTCAGGCACATCAGAAATCTGTGGATGTTTGTGTCCTAAAATAATACATTTGTTAACATCAAAGACCTTGGATTAAACTACCAGGAGAATTTATTTTAATGTCAAAAATAACCATAAAATAGGATTATATTGTTGAGTAACTTTTTTTTGTATCTGTGATCAGAAAAATATATTCAAGGTGTTAAAAATAAAAAGCAAGCTAATAATATTTTGCATACAGTGATATAGCAGTGACAGGCTAGATTTTTGGGGGACAAAAATCTCTAATTCTAGGAAAAAGAAGAGAATGATTCCTACAGAGAGCCTTCGACATTTGCAAAAGTACAGCATAGGTGAATTATGCAAGTTGGAATTTTACTGTCACATTATAAATCTTAGGTTGAAGAGTACCCAAAAGTAAAAACAGGGTAATGAGTTATATTTTAAGAATTAAAAATGGGTTCTGGAGAGATGGCTCAGTGGTTAAGAGCACTGACTGTTCTTCCAGAGGTCCTCAGTTCAATTCCCAGGAACCACATGGTGGCTCAAAAACATCTGTAATGGGGCGATGTCCTCTTCTGGCATGTCTGAAGACAGTTACAGCGTCCTCATATACATAAAATAAATAAATAATTTTAAAGGAATTGTAAATTCTAATGAAAAGCACTCATGATAATTTCTTATGAAAGCAATATTCATCTCTCTCATATTTTCATTTAAAAAAATAAAAACTTTCTAGAACTTGAACTCTGGCAGTTTAGTGAAGGGAGTGCATGGCATTTTAACCTGCAGCAGCAGGTATCACAGCTGAAGGTGATGATTGATAACTGTCTTGCCACTCTGCTGTGTGGCAAGCTGTGACATCTGCCACACTGTCAACCTGCCATCTCAAGCTGTCGAAATATGAATGGTAATGGTTACTGTGGTGAAACTTCAGTTATAGACAATGAGCTCTGACATCAGCTGGCTGGATCTCCTTCCTTTCCAG
Seq C2 exon
GAAGTATATGGTGCTGGTCCCTTCTCAGCTCTACACTGAGACCCCTGAGAAAATCTGCCTCCATTTATACCATCTGAATGAGACAGTGACCGTTACAGCTTCCTTGGTATCTCAAACGGGAAGGAGAAACCTGTTCGATGAGCTTGTGGTTGACAAGGACTTGTTCCAATGTGTTTCCTTCATT
VastDB Features
Vast-tools module Information
Secondary ID
-Cpamd8:NM_008646:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
No protein impact description available





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:
ENSMUSP00000080469





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Conservation


Human
(hg38)
chr12:9203952-9208258 
ALTERNATIVE
HsaINT0135660
(PZP)
Human
(hg19)
chr12:9356548-9360854 
ALTERNATIVE
HsaINT0135660
(PZP)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr5:101298283-101300709 
LOW PSI
BtaINT0010507
(A2M)
Chicken
(galGal4)
chr1:75747132-75750807 
LOW PSI
GgaINT1001721
([1])
Chicken
(galGal3)
chr1:79388273-79392546 
GgaINT0103734
([2])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ACAGTGTTAAGGAGGAGACACCA

				
R: 
AATGAAGGAAACACATTGGAACA

				
Band lengths: 
327-1688

			

		

	





	
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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