Special

MmuINT0023109 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr7:30628955-30631583:-
Coord C1 exon
chr7:30631488-30631583
Coord A exon
chr7:30631268-30631487
Coord C2 exon
chr7:30628955-30631267
Length
220 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
ACTATGAATTTATCTTTCAGACA
3' ss Score
7.99
Exon sequences
Seq C1 exon
GACTTTTTGTTTATCGGCCACATCTGTTCTCCTTGTTGGAAAAAGGACAAGACCCCTGGATGATTTTGAGGGATGAGACAAGGGGACCTTATCCAG
Seq A exon
GTGAGTGAGGGCTGGGGTGAAATGGGACAGTCATCAGATAAGATGATGGCTGTCTTAGAGTGCCGGTTGCTATGGTGAGACATCATGACCAAAGAGCAAGCTGGGGAGGAAAGGGTTTATTGGCCATTTTTAAAGCCATTCATCTTATACTCTAGTATTTTCTCTATTTATATTGGATGCTTTATCTGTTTTGAATAAACACTATGAATTTATCTTTCAG
Seq C2 exon
ACATAGATTTCAGTTCTCAGAACAAGAAGTTCCTGGGAAAACCTAGCACATATGAAGAATTATCTCAAAGGGAAATGAAGGAATATTTTAGAAAACGCAGTCTTGAAGATTTCTGTTTTGGAGATGGCTGGGATGGCAAAAATCAGTTTCAAACGCATCAAAATCAGGAATATTTTAAGCAACTGGCAGTCGCCTATGAAAAAGTGCTCACTGTGAACCAGGGTATAGTTTTCAACAACCACCAGAGACTGAATGCAGGAGAGAAAGCAACTGAAATTCAGTGTGAAAAAGCCCTTACTGTGGAATCTGACCGTATTCTTCCTCAGCTAACTCCCCCTGGTAACAAAGTCCACAAAGACAAGGAGTGTGGGGACACCTCTGCTCCTGAATCGGAGCGCACACACTGTCAGAGAGCTCACTGTCCCCAGACCCCTCAGCAGGGGAAGGAATCTGGAGGGCCGTTTGGTTTGCCTTCAGGAATACTGGGCCTTCCGCAAGGTCACACTGGTGAGAAGTCCTATGACTGTAAGGAGTGCGGAAAGTCCTTTACTTTGAAGTCAAACTTGACGCGACATCGCAGAATTCACACCGGTGAGAGGCCGTACACGTGTCATGGATGTGGAAAGGCGTTTACACAGAAATCCCATCTCATGTCACATCAGAAAATTCACACTGGAAAAAAAGCTTATGTCTGTGGGGTCTGTGGAAAAGCTTTTCACTGTGACTCAAGCCTGACCAGTCATCAGAATATTCATTACCATGCAGCTGATGCTGGCAAGAAAGCATATGAATGTAAAAAGTGTGGCAAAGATTTCGATTGTCACTCAGGTCTCATTGATCACCAGAAAGTCCACACTGGAGAGAAACCTTTTAAATGTAAGCATTGTGGAAGGCTTTTTAGGTTTCATTCACATCTTAGGGCGCACACACGGATTCACTCTGGCGTGAAGTCCTATGACTGTAAGGAATGTGGAAAATCCTTTAATTTGAGGTCAAACTTGATGCGACATCACAGAGTTCACACAGGTGAGAGGCCGTACACGTGTCATGGATGTGGAAAGGCGTTTTCACAGAAATCCCATCTCACGTCACATCAGAAAATTCACACCGGAGAAAAAGCTTATGTCTGTGGAGTCTGTGGAAAAGCTTTTAGTCGCGGCTCAAGCCTGACCAGTCATCAGAATATTCATTACTATGTGGTTAATGCTGGCAAGAAAGTGTATGAGTGTAAAGAATGTGGCAAGGCTTTTGGTTGTCATTCAAATCTTAGTCGCCATCAGAAAATCCATGCTGGAGAGAAACCGTTTAAATGTAGGGACTGTGAAAAGGCCTTTGGTCAAAGAGCACATCTTACCAAACATCAGAGAATTCACACTGGTGAAGAAGGCCCTGATGAATGTCAGAGCGTGGAAAAGTTTTTCCTTGAAGACCACAACTATGTCGACATCAGAAAATCCATACTGGTGTGAAATGATGGAATGTATGAGGAATGTAGAATGTGGCTCTTATTCGTGGTTTTTATTGTACCCACACTGGAATATTCACATTAGTGGCAAGCCCTGAGTCCCAGGGATGTGGGAAAGTCTACATCTGGAGTGCAGGCTTAATTGTCACCAGAGCATTCATACTGAGGAAAGAAAATAGTCCAAGGAATATGGAAAGACTATTCATGGTTTAAAGCTTAAATCATCATCAGAAAATATGTACTGTGGAGGAGGCTTAGCAACCAGGCATCTCCACCATCAACCTCAGGGACCCAGGGATCACAGGATACATCATCACCAGCTGCCAGGATGCAACGCACTCTCACCACATCCTTTGCAAGCACGTGTACAGCATGCTCTTATAAAAAGCCAGTGCCTCCTTATAGAGAGAATCCATTGTGTACTGTGTGGGGTCATCACCCATCAATAAATAGCTGAAGGCCTATTAGCTGAAATAGAAGGAAATTAGCAAGAGATAGAAAGTGGAACATCTGGTAGCAAAAGATTTGAACTTTGGGAGTTAGACAGAGGCAGGAGATTCCCTGAACTCTGGAGGAGACAGAAGCGTGAAACCGAGGATAGGCAACTAACAACAGTTTAACAGTTAAGTAAGTGACAAGCTAGTCAAGGAGCAACCCCAAGCTTATCAAGCAGCCATTTATTCATAAGAAATTAAGTCTCGGAGTCATTGTTCTAGAAACAAAGAGGCCAGGTAGAAAAGCTCGAGGCGAGGCTGCACCTCCTCTCCCTGTTCTTTTCCCCTCCACCCTTGCCCAGAGGCAGCCTCTGTATGCTCCCTCCTCAATAAACCTCCCAGTGAGACCTGTCA
VastDB Features
Vast-tools module Information
Secondary ID
-BC027344:NM_173738:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





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:
ENSMUSP00000082947





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000072378, ENSMUSP00000089115
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr19:36820115-36823284 
HsaINT0188416
(ZNF790)
Human
(hg19)
chr19:37311017-37314186 
ALTERNATIVE
HsaINT0188416
(ZNF790)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr18:47807958-47811054 
Chicken
(galGal4)
chr18:31475-31583 
ALTERNATIVE
GgaINT1030522
(ZNF302)
Chicken
(galGal3)
chrUn_random:28986233-28986335 
GgaINT0001428
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CGGCCACATCTGTTCTCCTTG

				
R: 
TACCCTGGTTCACAGTGAGCA

				
Band lengths: 
307-527

			

		

	





	
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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