Special

MmuINT0027895 @ mm9

Intron Retention

Gene
ENSMUSG00000020882 | Cacnb1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:MGI Symbol;Acc:MGI:102522]
Coordinates
chr11:97878037-97881080:-
Coord C1 exon
chr11:97880994-97881080
Coord A exon
chr11:97878157-97880993
Coord C2 exon
chr11:97878037-97878156
Length
2837 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACC
5' ss Score
8.66
3' ss Seq
CTGGTCCTCTCTGCTTTCAGGGC
3' ss Score
12.02
Exon sequences
Seq C1 exon
GGCAAGTACAGCAAGAGGAAAGGGCGGTTCAAAAGGTCAGACGGGAGTACGTCCTCGGATACAACATCCAACAGCTTCGTCCGCCAG
Seq A exon
GTAACCTAACCGGGAAGAGGGCTTGGGAGACGCCACCGGTTGGTGCAGGTTGGCTTGCGACTTTCTCCAGGCACCTTTTCTTCTGTCACTTGTCACCTACCTGGAACCACCACGCCCCGCCACCCCTTGACCTCTCTGCACCCACTGCTTCCGCCTCTCCTCCAGCACCAGCTCCCAGCCCCTGCTGCCTGCCCCTGTTGCCTGCCTGCCTGCGTCATCTCATTCAGGGACAGCCTGGCCTGCCTCCTCCTGGCTTGCTTTGGGCTGTCACCCACTCCCCCTGCCGGCTGTCTGCTTCCACATCCTCCCCCAGAAACTGTGATGGGGTGGGGCTGAGGCAGGTGCCTGGAAATAAGCTGAGATACCGGGCCCTAGTGAGGGATGGGTCAGGGAACATATTCTCTCCACTTCCAAATATGACTCCTTTTAAATATGCAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCAAGATGTTAGATAAGGGGTGTTTTATTTTAGAGGGATGTAGCCTGCATCCCTAGCTGAAGTTGGTGCTGACAGTAGTTCTCTGGGCCCTCATGCTGAGCTGGGAAAACTGCCACTTCCCTCTCTTCCCTCAACCCCAGGCCATCTTAGGCTGGGGAGAGGCAGTGAGGAGGCATGTGGTTGCTATGACTACTGAGCATCTCAACAAAGACTGGTACCCAAAAAAGGCAAGAGGGGCTGGGGATCAGAGAAGAAAAGGAGTGTGGCTAAGGAGATAGTAGACAGAGCGTGAGAGGGCAGAGGACACTTGGTAGGAGGAGGCCCCTGGGGCGAGCCCTGCCGGGTCCAAGCCGACTGAACTGAGTACTTCCTTTTTTTTTTTTTATATTAATTTATTTTTTACACTCCATATTCCATCCTCCCCCACCCCCACCCCCTGAGTACTTTCTTTTTGATTCTTCTCTCTCTGGGTTTTTCACGTGTGAGCCCAGGCTTAGCTCCAGATCCTGAAGGGAGGTTTTGATCTGAGTGTGTCTAAAATACACAAACAGATCTGAAGTTCTTTCCTTAATCATTCCTTTAGCCCTGCTGTTCCAGAGCTGGCCAGTGCCAGGCCTAGAAGCAGTGATAGCATGCTTCTGTGGTTGAGGCAGAGAGAGCCTTCAGTTTCCCCCTTGTCAGCCAAGGGCTTAGACCCCCACAGGCTCCTTCTTCCCAGCTCCCCAAGTCCTACCCCCAGTAGGTGGCGGGAGTGGGGGGCAGACCTTGCCACATCTCTGAGCTAAATATACCCTAGCAGTTTGCACATGTAGCAATTCTGCTTGTAACCTGAGCTCCTGGGGGAACCGGCTGTGTGGGCCACCCCTAGGCCGGCAGGGCCCAGGCACTGAGGGCGCCGGGATGGAGGTGCCCAGCCGGACCCTGGTAGTGGTGAGCTGGGGATGGGGCAGGTGGTGGGTGGGTGGAAGAACCCCTCAGACCGCTGAGGAGGGCCTTTCTCCCAGCTCATCTCTTCGCTCCTCTCCTCTTTCCTGTCTCCCCTTTCTGATTGTGTGTATGTGCGTGTATGCATATGTGAGTCTGTTGGGGTCAGGGGGTGTCTCTGTCTCTCTGGGCATCTGTATTCTTGTTTTGGGGGGCTGTGTAACAAGGGAGAATGAGGGTTCTTTTGCTTCTCCCTCCCCCTGGTTTTGTGTCTCTCCAGCTTTAATTAGTGACTCAAATCTCTAGCTTCTCATTCCCAGGATTTTCCCTAGGAAGGTAATGCCTGTATCACCTGATGATTTGGGGAGAGGTAGGTCTTGGCCTCCGTCTCCCATGCCAAAGCAATGGACAGTCCTATCCAAGTGACTCTTTCCTGCCCTCAGGAGAGATCCCTCACATACCTGTAACTCCACGTCTTCTCCATATCCCCTCCCACACTTGTCTGCCACCCCCTTCCCTCCGGAAGTCACACCAAATCCATGCAGCCTGTCCTCTGCCACCCTTTGCCTCCCACCCTCAGGGACATAGACCTCTGGATCACCCTTGGTGACTCAGTTGTTCACACCCAGCACACACGGTGGAGGACATGTTCCCAAGCGTTCTTTTTGTATTCCCAAATAGACACACACACACACATATCTGCACACTCATGACCAGTGCTATACACTTCTGTATAGCTTCCATGTGTCTCATATGTATATGTGTGTCTGTACCAGAGACCTTGGCACTCTGGGATGGTGACTGTGGTCTGCATTGGGTTCCTGTCACACTCAATCTTCACAACTTGACTTTACCCTGCAATCTAGCAGCCTAGTGTCGGGGCAGAGACCTGGTCCATCTTCTGCTCTCCCCTCACACCTCCTGCTGAACTGCCCTGAATAGCATAAGGCAGCTTGGGGTTGCCTCAGAGTGGCCCTATTCAGGAACTCCCAGCTAGAGGGGGAGGGATGGTGTCTTGCTTCCCCCCGATCCTCAATCAATGATTTTGGTGGCCCTGTCATTCCAACAGACCACCCATGGGCAACCGTGAGGATTCAGGCTTAAGAAGGTGGCTACAGTCCCTGGAAAGGATGGCGTTGAGTTTCTGCTATGCCTCCTCGGCCATTCAGGGGCAGGGCAGAGAAGGAGGAGCTGGGAGTTAGAGTCACCCCCTGGCACTCCTCCCTTGTGCTGTGCCCCTATCAGATTCCCACCCCTCCCAAGCCCCAAGCAGCTGTCATTAGACCTGCCTTAACCTCCAGCTGGTTGTTGTCACCTTTCCTAGGGTCACACTCATCCCACAGGCCTGCAAACTTTGACCCCTGGTGGCACCTCTATGTGGTCCCAGGAGCCAGGAGAAGTGGCGCTGGCCTTCATCTGGTCCTCTCTGCTTTCAG
Seq C2 exon
GGCTCAGCAGAGTCCTACACGAGCCGACCATCAGACTCTGATGTGTCTCTGGAGGAGGACCGGGAAGCCTTAAGGAAGGAGGCAGAGCGCCAGGCCTTAGCCCAGCTCGAGAAAGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020882-Cacnb1:NM_145121:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=0.883
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF120523=VGCC_beta4Aa_N=PU(92.9=97.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000099433





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000017552, ENSMUSP00000090412, ENSMUSP00000103187, ENSMUSP00000128095
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:39191594-39194883 
ALTERNATIVE
HsaINT0026545
(CACNB1)
Human
(hg19)
chr17:37347847-37351136 
ALTERNATIVE
HsaINT0026545
(CACNB1)
Rat
(rn6)
chr10:85968958-85971867 
LOW PSI
RnoINT0028222
(Cacnb1)
Cow
(bosTau6)
chr19:40298345-40301314 
LOW PSI
BtaINT0030526
(CACNB1)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr7:36977983-36978037 
Zebrafish
(danRer10)
chr3:16044876-16067956 
LOW PSI
DreINT0040129
(cacnb1)
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"