Special

MmuINT0029997 @ mm9

Intron Retention

Gene
ENSMUSG00000040213 | Ccbl2
Description
cysteine conjugate-beta lyase 2 [Source:MGI Symbol;Acc:MGI:2677849]
Coordinates
chr3:142394166-142397624:+
Coord C1 exon
chr3:142394166-142394255
Coord A exon
chr3:142394256-142397437
Coord C2 exon
chr3:142397438-142397624
Length
3182 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
CACCCTTTGTTAACGTGCAGGCA
3' ss Score
7.49
Exon sequences
Seq C1 exon
CTCGGCTGGAGCATTGGCCCTGCTCACCTGATAAAGCATTTACAGACCGTTCAACAGAACAGTTTTTACACGTGTGCGACTCCTTTACAG
Seq A exon
GTAAGTGTTAGCCTTTATGCCTGCGCAAACTGGACAGCCTCTGCATGAGCGAGCCCTTCTACTACACCTTGGGAATTTTGGAGCAGACATGTAGCCTTTGGATGCACCCCTAATTTCAAGCTGCATAATTTATGTCACATTTAAAAAGCTCCTCTTACCATACAGGATAGTATGTTTTAAGAGACAGACAACTCTGGTGGTCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTACTGCAGTAGCTATTTAAAAGAAAAGAAAACCCTGGGTGTGGTGATGCATGCCTGTTATCTTAGCTCTTGAGGCTTCAGTCGGGAGGAGCATGAGTTCAAGGCTAGCTTAGACCACACTGAGACTTTAAAGCATGGCTGGACAACAACATACTAGGGCCCCGTGGAAACAGACCGAGGACACACAGTACAACTATTCAGAAAGATTTCCAGAATATATCGTGAAATTTTTAAAAAATGAAAATCCATGGCAGTATGTATTGTCTATTAATTTATACTATATTCTGTGTAAGAGAAGTGGGATGCCTTCTTAGATGATCCAGAAGAAAGCAGCTCAGGGCTGCCTGTGTTGGTAGAACTGGCTGATGGGAAGCAGACAGCAGATCCATTCTCCCAGGTTGATCTTTCTCTCTAGCACAATGCCCTGCCTTAACCTCCCACGCTGTGGGAGCACAGGCAAGTACCACTATTTCTGGCCCTGGATGTAGAGCTTTGTTAGGCTGTTGCTATTTTTGTATACATTTCTAGAAACGGATCTATTTACCATCCTCCTCTGAATTCCCCAAACAAACTAAAACAATATTCTACTTCTAGGAGGAGCGAAAGCACAAGAGAGTAAAAGTATCGGTGTCTACATCCAATCAGTGGTTGAGTGTTTCTCATCCAAGTTGTCTGTCTACCGAATAGGAAAAATTTCCATTCTTTTTAGTGATTCTCCTAGCTATGATAAAGGCTAGTTCTGAAGGTTTGCTTTATTATATTTTAAGTTCATTTTATCACCTCAAAACAAAGACATTCACTTATTCAACTAAGATTTACTGGAGATTAGAGATTTTACAGACAAAAAGCCACTGGACTCACATAGCTTAATACCTAGTCAAGAGACATAAATAATAGAGATACTTTTAAACAATATTATGTTAGACTTGATAGATGCAAAGAAAAGGTTGGAAGGAAGGCAGATGTAATGACCCAAGTTGGAGAGGACATGATGTCATATTGGACTAGCCCCATGGAGAAGAGAGCATCTGAGCACTGGTTAACCTAGAGAAGAGCCCTGTGGTCAGAGAGACTAGAAATACAACCCAATGGTAGACAGCATGGCTGCCATGGGATGTGGGAAGCCATGGCAGTTTTGAACGTATGCTATTGAAAGGAGTCTGGGGCTTCATGGAGGGAGAACATAAGAGAGGAGTTACCAGAGAGAAATATCAGAGGACTGAACTGAACTGAGGATGGCAGAACTGATGGGGCCCTGGACACAGTTGGAAGATTAAGTCAGTGGTGCCTGACACTGGGCATCGCAAACATGCTTGGGAAAATGAGGGGGTCCCAGTACACTCAGCACAGATGTTTGTGTCTTTGTGCTTTGGATTTTCCAGGGCAACGACTTCTAGAGTAAATGAACAAACTGCTCAGAAAGGTACAGCTGAAATTCTATAGCATTTCCTGAAGCATCTTATTCTGCATTTCAGGAAAAAAAAATGTGCTCAGATAGCTATGTTTGGAAACTGGATGCTGATCTCCTAGTGCTAAAAAGTTCTGTCTCCTTGCTAAATTCTCCTGCCACAAAGACTTACATGGGATCTCGACCCCTCCTACCCGGTCTTGCTCTGTCTTTTGCTACAGCTCTGTCATACATAACAGATTTTCTTTCCTGGCCTTTCTACCTCACCTCCTCATCCACCCTTCAGTATATAATTATGAAAGCCAGGGCTTTGCCTATGATGTTAACCATTCTATCTCCAATGCCGGAAGCCATCGGGCATGCTTTGCCTGCCAAGCATCTCGCTCTCGGCTTGGCAGATCTCTGTGCTTCATGCCCACTCTGTGACTTGTTTTTATTATCCTGACCTGCCATGCTTCTCAGCCACATGCCTGATCCTTACTGACACGTTGTTGTAACAAAGTACTAGAGACTGAATAGCCAATACAGAAAAGGAATTTAGGTACTAGAACGATGGCTCAGTGGTTAAGAGCAGTGGCTGCTCTTCCAGAGGTCCTGAGTTCGATTCCCAGCCACTCCATAATACCCTCTCCTGGTATGCAAGTGTACATGCAGATAAAGCACTCATACACATAAATGAATACGTAAATTAATTGATCTTGAAAGAAAGACAGAAAGGGAATTATTTCTCATGGTTCTGAAGGCTGGGAAGACTCAGATCCTGACCCTGCCTTCTAGAAGCCATATCAGAAGGACCTGCTGCCTCATAGGTGTCTCTTTTTCATTGTGTTCTCCCGTGATGGAAGTGGTTCTGGTACCATTCCTGGGGCCCCTAGTCTCCTGGGCCTAATCACCCTGCAAAGGCATTGGGAGTAATGCCTATACCTGGGAGAACAAATTCACCGAATGGAATGAAGGGAACACGAACATTAAGTCCTTTGCTCTTTACAATCTGGTTTTCCTTGGTCACATTTTCTCTTCTTTGCCACCACTGCTGAAGAAGTTACCCACAGTTCCCGGAGATTTGTCTCTAGATACATTCACTCCTTGGGACCAGAATGGTTTCAGTATTTCTTCTGAGGAATGGGGAACTCGGGTTTGCTTGTCTAGACAGCAGGCCAGGTTTAATTTCCTCCAGTGCCTTCATCAGGAAAGACTCACTCCCTCTTCCCCTGTCTAGCCATTCTTTGAGACTTAGCAAGCCGAACCACAGCTCATCTCATTAGAAAACTCTTCATGTCTGTTTCTTACCAAGTACACCATCTTTACATAACAGATCGTTTTCAGTTGGGATTTTGGTGTCTTCCTCTGTTTGTCATATTAGAGTCAAATGTTTACACCAAAAAGTCCTTCCGCCATTAACCTATGGAGCTGAATCGTCCATGGGAAGCTGGCTGTAATTGACCGAGTGACTTCTTGACACAAATCTTAGTATGATGATCTTTATTTATCCTACCAGGGAATTAAGCCATAACTGACACCCTTTGTTAACGTGCAG
Seq C2 exon
GCAGCCTTGGCCGAGGCGTTTTGGATCGATATCAAGCGCATGGATGACCCTGAGTGTTACTTTAATTCTCTGCCAAAGGAATTAGAAGTAAAGAGAGATCGGATGGTCCGTTTACTTAACAGCGTTGGCCTGAAACCCATTGTTCCTGACGGGGGTTACTTCATCATTGCTGATGTGTCTTCATTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040213-Ccbl2:NM_173763:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0015516=Aminotran_1_2=FE(7.6=100)

							
A:
NA

							
C2:
PF0015516=Aminotran_1_2=FE(16.2=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000101825





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000041675
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:88949278-88953062 
ALTERNATIVE
HsaINT0028675
(KYAT3)
Human
(hg19)
chr1:89414961-89418745 
LOW PSI
HsaINT0028675
(CCBL2)
Rat
(rn6)
chr2:248676272-248679936 
LOW PSI
RnoINT0081189
(Kyat3)
Cow
(bosTau6)
chr3:55137580-55140631 
LOW PSI
BtaINT0032429
(CCBL2)
Chicken
(galGal4)
chr8:14088337-14089016 
LOW PSI
GgaINT0038345
(CCBL2)
Chicken
(galGal3)
chr8:15846524-15847203 
LOW PSI
GgaINT0038345
(CCBL2)
Zebrafish
(danRer10)
chr6:25275097-25275169 
DreINT0042131
(ccbl2)
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
  • 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"