Special

MmuINT0027891 @ mm9

Intron Retention

Gene
ENSMUSG00000020882 | Cacnb1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:MGI Symbol;Acc:MGI:102522]
Coordinates
chr11:97880994-97883941:-
Coord C1 exon
chr11:97883656-97883941
Coord A exon
chr11:97881081-97883655
Coord C2 exon
chr11:97880994-97881080
Length
2575 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TTCCTTCCCCACCTCTCCAGGGC
3' ss Score
9.9
Exon sequences
Seq C1 exon
GACGGCGGCAGCGGCCGCAGAGAGCACAGCGCGAGCCGGGAGGGCAAGCAAGGCGGCGAGCGTGCAGCCGGAGGTCCAGCTGGGAGACTGCACCCGGTGCTGGCTGCGCGACGCCGCGCTGCTCTGGGCTCGGACGGCCTCTCCCATGCGCTGAGAGCGCCCGGCTGGGCTGGGAGGGCGGCCGGACCGGAGGATCCTCTCCATGGTCCAGAAGAGCGGCATGTCCCGGGGCCCTTACCCACCTTCCCAAGAGATCCCTATGGAGGTCTTCGACCCCAGCCCACAG
Seq A exon
GTAAGGCGAGGTGGCAAGCTCGAGGGAAAGGGCCGCTCCTACGGATCTTGGGGTCGGCTTGGAAAGCCCCGGGAAGGAAAGGGTTATATGCCCCGCGTGGATGGGAGAGGGGTGTCTGCGCGACCCTCCATTCTCGAGGGTTAATGATCGATGGACTATTGGTCCGAGTCGGGTTGCGGTGCTGCGGAGCGGAGAGGAGGCGGTTGGAATGCCTGTCAACCTCGCCTCCAGGTCTCCCCCGCGTCCAGGTTCCTGCTGCTGGGGTACTGGCTCCAGCAGGCTGACAGCGGGGATGCTGATGGGGGTTGGGGGGAATCCAGGCCTTGAGAAGCGGAGTTGGAGGGAGGCTGGAGAGCGAATCGGGCGAGGGGGGCGACGCAGAGCACGTTTAGGGGCGCTAGTGGGTGTGGGTGGGGCGGGGGTAATACTGGGAAAAGGCCTAGACGATGGTCAGAGGGCGTTGCCAACAGGCCTTCGAAGGCTCAGACATTGGCTTTCGAAGGTGGAGAAGAGATCAGCTCAGGGAGGCCCTCCCCTAGTCACCTGGTCTCCATCCCTGTCTTGGATGTTTCCCTACTCCCAACACCCACATTAGCTTACCCCACCCCCTGCCCCAAGGGGTGGGAGCCGCCAAAGTTTGGAAAGTTGGATGGGTGCCAACTCACTGTCTTGGAGTGGAGGTCGCTGTTTTACCTGGGGGAGGGGCGCTGCCCTCTAGCACGTTCACTTTTCCTATGTGCCTGGGTTATTCCTAGGTAGGGGCGTTCTTGGGCATACAAGGTCCCCCTAGAATGACCAGCAGGGCATGTGGTGGCCATGCCAGGGGATTTCTCTAGGACTTGTCCTTCTCCAAGGATAGCATTAACACTTGCATTGCTGTGGCCAGCCTGGAGCAACTGTAAGCAACATGATGTGGTTGATGGGTGTGTATGGGGGGGGGGGTCAGGTCAGACCTAAAAATACTTCGTCTCTCCACCCCAGGCCCCTTGGAGTCTGGGAGGCAGCTGACTGATGCCTTCCTTTCAGCTGTCCCCTGTCCCTCTGAAGGCCACTCCCTTTGCCCAGCTGGGGTGAGGTAGTGCTGTGAAAGAGTCTTGAGGTTCACTGTAGAATGCTCTTAGGTCTGTAGAGAGCCTCAAAACTAGTTTAGCTGTATGCTCAGTTTTAGAGAAGGAAAGAGGATCATAGAATATTCAGTCCTATTATTCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGATAGAATCTTATATAGTCAATGCTGGCCTTGAACTTATGATCCTCCTGCCTCTACCTCCAAAGAGTAGAGAATCACAGGTGTGAGTCACTATGCCTGGCTCACCAGCTTCCTTGTCACCAGGTCTCAGGAGCCAGAGCCTGCAGTGTCGCTGAGGTGCCTCTAGGCTCTTTGGTCAAAGAAAGTCTGGGATAGAGGTTAGGGGCAGGAGCTTTTGGGCATTCTGCCCATCCTGTACTGGGCAAGGGCCAAGAATATGAAATATGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGAGGGGGGCACAGAAGCAGCTCCCATATAGGAAGCAAAGAGACACTCAATGCCATAACTTTGGCATATGAGAGGTCAGACAGGATCCCCCACCCCAGTTAGAGCCCACTAAGAGAGATTAACCATCTTACCTGGTACTGGCAGGAGTATATGTTCTAGTCTCAGCTTGGGGTGGGGCCACAGGGCCTTTAGATGGATGGAGCAGGGTTAGTATGATGGGGATGGGGCATGGGCAGTAGCAGCTGGCGTGGGAGTAGAGTGAATCCTGCCTTGGGGGGGAATATAAACACTGATTGCCAGGACGGAGGCTGAGAGAAAGTTCTGCTAGGGTGGAGGCAGAGTGGGAAGCTGAGCCTACTCTGAGGCACCTAGGCACCGGCCACAGGTTGGATGTTTAGTTTCTCCGGATGTGGCTGTTCTCTACCTCCTCCCTCTTTTCCTTCCTCAGAAATGTCTTCAAGCGCTGAATGTCTTTCCCTCCCTACTCAGGGGCTCAGGGGAGGAACCAAGCCAGGCCCTGGGTTGCCTCCTCTCTCTGGGGGCACAACACACACTCTGCCCCCTCAGCTCCAGATACAGGGGAGAGGACATCCCCCTCTCTTCCTCCACCCCCCCCCCCAGCACTGCAGGCAGCCTCTCCCTTCCCTGGAGGCTGCTGCAGCCTGCCCAGCATCTTAATTAGCTTTGCTGCCTAATGAGCCTCCCGTTCCTCGGGCCTTCTGCTTCTCAGCCTTCTGCTTGATTTGGGGGATTCCTGTGTGTGCATCCCAGGCTCGCTTGCAAAGGTTCCTCATGGTGACTGTTGTCTGGGCATTGTCAGTGAGGTAGAAGACCCTCTTTCCTTTCAGGCTAGCCACCTCTATGGAGGAGAAGCTGAGGACAGGGGTGGGGCCAAGCAGAGCGTCCGTCCCCAGGCTAGGCTGGCTGTATACAGCAGCAGCCCTGGTAGGAGCTGAACTAGGAAAGCATCTTTCTGATTTGACTCTGGTTCCTTCCCCACCTCTCCAG
Seq C2 exon
GGCAAGTACAGCAAGAGGAAAGGGCGGTTCAAAAGGTCAGACGGGAGTACGTCCTCGGATACAACATCCAACAGCTTCGTCCGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020882-Cacnb1:NM_145121:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
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)
chr17:39194971-39197411 
LOW PSI
HsaINT0026541
(CACNB1)
Human
(hg19)
chr17:37351224-37353664 
LOW PSI
HsaINT0026541
(CACNB1)
Rat
(rn6)
chr10:85971955-85974497 
ALTERNATIVE
RnoINT0028217
(Cacnb1)
Cow
(bosTau6)
chr19:40296564-40298257 
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr3:16068044-16077597 
LOW PSI
DreINT0040125
(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"