Special

MmuINT0036546 @ mm10

Intron Retention

Gene
ENSMUSG00000029516 | Cit
Description
citron [Source:MGI Symbol;Acc:MGI:105313]
Coordinates
chr5:115938679-115941932:+
Coord C1 exon
chr5:115938679-115938804
Coord A exon
chr5:115938805-115941836
Coord C2 exon
chr5:115941837-115941932
Length
3032 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
GACTGCTCTTTTGTGTCCAGGAG
3' ss Score
7.99
Exon sequences
Seq C1 exon
GAACGCCGCCACTCCCTGGAGAACAAGGTAAAGAGACTAGAGACCATGGAGCGTAGAGAGAACAGACTGAAGGATGACATCCAGACAAAGTCCGAACAGATCCAGCAGATGGCTGATAAAATTCTG
Seq A exon
GTGAGCAGGAACCAAAGGTGCAAAGTTAGCGGTCTCACAGGGAAGGGGGCAAGAAGGCTCGCACGCTGTCCTGTGGGGGTGTCACTGCGTAGGTGGATGGAGAGAGAGGTGGTGTCAGAGAGAGCCACCTGCGGAGTGGAACGGATGAACCAGGCCTGGACATCTTAGCACTAGTGACCAGCCACTGCAGTCTTTACTGTTCCCTGGTCTGCTCTCACCCGGCATCTTAAAAAATGGAATTGGGCCTTTGTCATGTGACTCGTTCACACACCCTCCTCTCAGCAGAGTTCTGCTTGGCTGTTAATTCGGCAAAACCAGTGCAAAAAGCTACTGGGGCTTTATAGACAGCTACGGCCCAAACTCAGATTCTCACTCTCAGAAAGGAAAGAAATGAGTCATGCGGGTTCCCTCAGAGTAAGTAGTATCCGCCCGGGGTGGCTCTTCACCCACTCACCCCGCTGGCGGCGGCGGCTGTGTTTATTGCCTTTCTCCTTGCCTCAGCTGGAGCATCTATCTCTTCATCACTCAGAGTCTATCTTCGGCACTGATGACCAAATTAACGTAACAAGGGGGTGTTGGCAGACATGTTGACTTATGTCCCTGGCCCAGGGTGAAGGACCGCCTTTGAGCCTCACTCCCAAAGTCAGAAGTTAGATGTCATGTCTGAGAGGCTCAGGGGTGGCTTGTAATTCATGCCCAATGCGCAGTTGTTCCCCCCAGAAGGAGGTGGGGATGTTAAAAGGCCACTTCATCTCTCCTGTCACTTCTGGGAAGTGGGATCCCCATGGGTGTACGTCCTCGAGGATGGCTGCCTTAGAGGTTTGCACAGTATTGACCCCTCATAGGTGACTCTGTATATTCACCAATGTTAAGTATGTTCTGGAGCAAATGCAGAGAAGAGGAGTTGGTCAAATTGTTACGCTTTGCCATCCAGTCTCTATATTTATGTGCATACGTGTGTGTGTCCGCACACAAAGACAAACGTGGATGTCTATTCTTTTCCGATCTCTTGTTCTGTCTTCAAAATCTCTTCTGGCCGTTGTCAGGCACGTGAGTTTTACCATGAGTGAAGACAAATCCTGCCACTGTTACCCTTTACCCGGCTAACCATCAACGAAAGGTTTCAATTCTTCTGTGGTTCCCAGAGGGTTTCCCTACTTAACGGTGACGTGTTCATTCATTCATTCAACAAATATTTAATGAGCTTCTACTATGCACCAGGCCCTGTTCCAGGGAGCTGGAAATGTAGCAGTGAACAGGGAGAACTGCTCTGACACATATAGAAAAAGAGACATTAAACAAATAACAACAACAACAAAGACAAAACCATCCACCCGGTAGTGAGGTGTGAGTGACCAGGCCCTGCGTTTTAGATGCTGCCCATATCCTTGTCAGACTCAGTGAGTGGTGGGTCTTCCCTTTAACCAGTTTATAGATCTCTATCCCTGTTTCTGTGACATCTTATGAGGGCTGAACCTGAAAAAAGATGATTAACAAGTGATTCGTAACCAGCAAGACAAGCAAACTTTCTTTATTTCCGAATGTACCTTGTTACCCACCCAAGTGCCTTCGTGCGTGGCTGAATGTGCCCTCGTTTTAACAGAATGTGCCTCTTGCTCAAGACCCTTGTGCTCGGGCTGCAGAGTGTACAGGACACGGGCCAAGAGCGGTCCTTCGTCCTGTCATGGACTGGTGACGCTGGGAAGCACATCCCAAATATGCATGCTCTTCCGATAAGAAATTTCAACATGTGTCATTGGGGCCCTCAATCATATAAAGGAGTCTTTGCCTCGGGCCCTTTCGCGCACATGCTCAAAGCCCGTAAAATGTTTTTATTAATTAGACTCCTGTTTATGTCCAATTTCCCTGGGAGCACGTCTGGTGGATCGCAGCAGATTTTGCGCACTTGGTCTTAATGGACAAGCTTGACACTGCAGAGTTGCGGGTTTTTGTGAGCATGTGACTCTCAGAAGCTCCCCCCAACAGCGCCCTCCTCCCCTGCCTTCTGTTTTGTGACGTATCTCACATAATTTCCTCATTCCTCAGAATTCTTCGTTGAAGAGAACGTGGGATATCAACTTCCCATGACCTCTGGTGTCCGTATTAACCAATGGGCCCAGATTCCTGGTTCTGTGCGGCCATGTCTGCAGTTAGGGTGCCTGCAGTGAATTGGATGCCGCCTTTCGTAAAGGGCCGGTTTCTAACACACGGGCAAATGAGTTGCCGTAGTTTTCTAACGAATCATGAGTTTTGTTGAAGGACAGACAGCCATAGAGGAAGCATGAGCGCCGTCCGCTCAAGCTGCTCACGCAACCCCAGTGTGTCTCCTCCTCACGCGTGTGCGCTGGCGTTTCCATGGCCACCGCCCATGTTCCCATTCACACACTTCACAGAAACACTAAGTCATGTGCCCATGTCTCAGGATTCACATCTCTACATTCCAGTCGTTTACAGGAGTCACTCACAATGCCAGGATTTTTTCCATACTTGCTAATTGTAATTGCTTTCCTTTTTGGCAAGGGTTCTTGAGCAATGTTTAATGAGTGAGGAAGACCTCACCCCTCCAATTGTTTATCTCCATAATACATCAGGACCCCTTTTCTTATTTAAGGCTGATGAACACCAACACCTCAATTAGCCTGAGGCTTAAGACAGTGGTCAGGGTCTTTGTGCTGTGCGGAACCTAATGCTGTCTTGTTACCTTTATTTCTCTGTGTAAAGTCAAGCCGCTGCCTGTCTTGGCCTGTCACACCATCTCATCTCTGATCCCAGCCTCACAGCCCACTGGCTCTGTGTGTGTGTGTGTGTGTGTGTGCTCGTGCTCGTGCGCGCGCGCGTGTGCGCACTGAGAGAGCCAGAGCCACGTGTGGTGCTGATTTCCTTCCCAAGAGCTTTAGTCTAGTGTTGCAGGAGCAACGGCTACCTGTCGCGTGCATTGCCTGTGGCAGTCATGGTCCCTGTGAGTGTCTCGTGCCTGCCCGCCTTGGTGCCCTTCCCCGAGCCCACCTGACTGACTGCTCTTTTGTGTCCAG
Seq C2 exon
GAGCTGGAGGAGAAACATCGGGAGGCTCAGGTCTCAGCTCAACATCTAGAAGTACACTTGAAACAGAAAGAACAGCACTACGAGGAAAAGATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029516:ENSMUST00000051704:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=0.803
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000099620





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000062049
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr12:119767183-119772769 
ALTERNATIVE
HsaINT0035525
(CIT)
Human
(hg19)
chr12:120204987-120210573 
ALTERNATIVE
HsaINT0035525
(CIT)
Rat
(rn6)
chr12:46399440-46402461 
LOW PSI
RnoINT0036638
(Cit)
Cow
(bosTau6)
chr17:57923707-57927033 
LOW PSI
BtaINT0038677
(CIT)
Chicken
(galGal4)
chr15:9598848-9601694 
ALTERNATIVE
GgaINT0008815
(CIT)
Chicken
(galGal3)
chr15:9863310-9866156 
LOW PSI
GgaINT0008815
(CIT)
Zebrafish
(danRer10)
chr8:3786594-3790424 
LOW PSI
DreINT0006308
(CDC42BPA)
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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