Special

MmuINT0027893 @ mm9

Intron Retention

Gene
ENSMUSG00000020882 | Cacnb1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:MGI Symbol;Acc:MGI:102522]
Coordinates
chr11:97867002-97870746:-
Coord C1 exon
chr11:97870595-97870746
Coord A exon
chr11:97867098-97870594
Coord C2 exon
chr11:97867002-97867097
Length
3497 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
TCTCTCTCCCCCTCCAACAGGTA
3' ss Score
11.9
Exon sequences
Seq C1 exon
CTGAGGTACAGAGTGAAATTGAGAGGATCTTCGAGCTGGCCCGGACCTTGCAGCTGGTCGCCTTGGACGCTGACACCATCAACCACCCAGCCCAGCTCTCTAAAACGTCGCTGGCCCCCATCATTGTTTACATCAAGATCACATCTCCCAAG
Seq A exon
GTGGGTGCAGGAGACTGGTTCTTATAGTGGACACGGTCTACGAGGATTGTTCTGGAGACGGGGTGCATGGGTCATGATGGGGTGACTTATGTCCTAGCCTTAGTTTCCTTCTCTGTAAGACTCATGGAAATTGGAACTACACAACCTAATATGGGTGGAAAGAGTCGGGTACGCTGTACCTTCTGTGTATTCAATATTGTAAATGTTATTAGGGTTACACAGGTCAGTCTCATCTCCAAACTTCCAGTCCATCATTGGGTCAGAAAAATGAAAGAACATGGTATAGTTTGTTCCAGTGTTCCACCCAGCTGTGTGGTGGTTGGAGAGTTTTGAATCTTCTAGTGTCAGGCTGTACAAACTTGCTCCTGCAGACTTTGACACAGAGGGTAGTGGTAGGGACCCCATGAACTTTCTCCTTCCTTCCTTCTTTAAAACAATTTTTCTTTTTATTCTTGTTAATTATGTATATATGTGTGAGTATGTGCATGTGAGGCCAAAGGCAGAGAATCTCCCTGGAGCTGGAATTTCAGGTTGTGAGCTGTCCCACAAGGAGGCTGGGAATCAAACTTGAGTCCTAACCACTGAGCCAGTCTTTCCTTTGTAAGGCAGGGTGGCCCTGTGTAGCTTGAACTTGCTATCCTCTGCCTTAGCCTGCCAAGTACTGGCATTCAGGCGTGTGTGACATACTCCTGGCTCCACGAACTTCCCTTTGAAGATGCTAGTGGATTTGAGAGACATGGGGGAAGGATTTAGGTGAAGGGTTCGTTTTAAAGAACCCTGCGGCATTTCCTTGAGCTTCCCGAGTCCTTGATTTCCACTGCTCTATAACTGTCAGGATGGGGTTTATATCCCTGAGGGTGGAGACGTTGCAAAGATCAAATGAGGTGATGGATGCAGAAACATTCTGTGGCCTAGAAAGTATCGGAGGTTCCGCTTCCTCCACCGAGCTTAAGTGGGCGTGGGCTCGAGTGCCTGGGTTTCCTGCCCTGGGCTGTCACTTAGCGTTACTGTGTTCTCCTGGCAACTCATGTAACATCTCTGTGCCCTAGTTTCCCCATCTTCTGCCTAGTCACGCTTCGGTGATCACTGTGAAAACTTAGTAAATGCATTAATTATGTAAAGAGCCTGGTGCCCACGCTGGTACCATATTCTTTCTGTTAGCTTTGTTTCCAGCTTTTAGGACAGGATCTCATGTAGTTCTGGCTTCTAATTCACTGTGCAACTAAGGATGGTCTTGAACATTTGACTCCCAAGTGCTAAGGGTTTAGGCACATGCTAGCATGTTCGGTTGGTTTGGTTGGTTTGGTTTGGTTTTTCTGTGTAACATTCCTGGCTGTCCTGGAGCTCACGCTGTAGACCAGGCTGGTCTCGAACTCAGATCCTCTGTCTTCCCAAGTGCTGGGATTAAAGGTGTATGCCATTGCACCCTGGTTCATCATGCCCAACTTTTTATGTTGATTCTGGGGTTCAAACTCTGGTCTTCAGGTTTGGGAGGCAAACACTCTACCAACTGAGCTACTAGTGATCTTGAGCCTCTGGTCTGCCTAATTCCACCTCCTCCATTGCTAGGAACCAAACCCAGCGTCTCATAAGTGCTGAGCAAGTACCGTGGCACCAAGCTATACCTCTAGTCTGATTTTATTTTATTTCAGTGGATGAATTTTTGCTCTCATTTTCATTAGCCAAGACTGGCCTCACCCCCCAGCCCTCCCGCTTCCGACTCCTGAGTACTGGGATGATTGCTATTGTGTCCAGCTCTGACTTTATTTCATTATTTTTGCTTATGGCTTTGTTTGACACAGGGTTCTATACTGTGTAGCCCTGACTGGATTGAAACACACTCTGTAAACCAGGCTAGGGTTACAGAGATGCTCTGCCTCTGCCTCCTGAGTTTGGAGACTAAAGGTGTGCACTACCACCTGGGCCTCTCATGTCTATTTTTAAGATAAATTATAAGCTTACATATACAGAGTGAGCCCCTAGATTCAGTTCTCAGCACACACTTAACAACAAATCTTATGCCTTCATTCCTTTTAAGACAGCATGTGTTTTTTTTTTTAAAGATTTATTTATTTTATGTATGAGTTCACCATAGCTGTCTTCACACACACCAGAAGAGGGCATCAGATATCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCTGGACCACTGGAAGAGAAGTTGGTGCTCTTAACCACTGTGCCATCTCTCCAGCCCCCAGCATGTGTTTCTTAAGGCCAGGAGCTTTCTGGGAGAGTGAGTCAGGAGGATCGGAAGTTTGGGTCAGCGTCAGCAACATTATGAGTTCATGCCTCAGTGCCTCCTCCCATATCCTATGTTATCTAAAAGTGGGGTGTACACCTTTAATCCCTGCACTCAGGAGGCAGAGGTGGGTGGATCTCAGTGAGTTCAAGGCCAGCTGATCTTCGTATCAAGTTCCAGGCCAGCTATAGCTACATAGTGAGACCCTGTCTCAAAAAACCAACCAATCAAAAAAGCCCATCCATATTCAGCTTTTTAAAAATTGTCCCAATAATTCCCCCTTATGATACCATTTTCCATAACCCAGTATCATACTGTGTGTCTTTTTCTGCCTTTTTTCCTTCTTTTTTAAAGAATGATTTTTTTATATATGCATTAGTATCTTGCTTGCATGTATGTCTGTGTCGGGTCCCCTGGAACTGGAGTTACAGATAGCCATGAGCTGTCATGTGGGTGTTGGGATTTGAACCTGGGTCCCCTGAAAGAGCAGCTAGTGTGTTCTTAACCACTGAGCCATTTCTTCAGGCCCACTTGGAGTCTTCTTAATATGGAGTAGCTCTTTAGCTTTCTTTAGATTTTTATGACAATGGTGGTTTGCAGTAGTATAGGCCGACCATGTTGTAGACTGCCTCTCTGTTGGAGTTCCATGTCCCTCCATAGCTGGAGTTAGTTTGGGGATCAAGTTTAACTTGATCATGTGAAGAAGCTACTCAGGAGAATAGACAGGAGGGAGCATTCTGCCTGCCGGTGCCCAGGGCCTGTTGGATACCAGTCTGGATGATATAGCAAGTCCTCAGCTCAAACACCAACAGCTTTGGAGCAAGGCTAGTATCCAGCTTTTGTTCATATGGAAAAGAGGGAGTGAGACTGGAGGATTAGGATAAAGTCTGTAGACAAGGTGTGTGTGTGTGTGTGTGTGTGTATGAGTGTGTTGCATGAATATTTGAGTATGTGCTCGTGAGTATGTGCGTGAGTGTGTGAGAAAGTGTGTGTGTGTGTGTGTCTGTCTGTCTGTGTGGCGTGTTGCCCTAAGCCTGAGCCTTGTGTCGTGGACACAGAGCTTGTGATCTCATTCTGGCAGAGAGGCTCAGGGCAGAGAATCATGGAACATTCCACCGCTCTGACTCTGACTTCCCACCGGCTCCAAGCAGAATCTGCCTTTTAGACTTGGGTGGTTGCCCGTGCCCTTCTAGCTCTCTCTCTCTCCCCCTCCAACAG
Seq C2 exon
GTACTGCAGAGGCTCATCAAATCCCGAGGGAAGTCTCAATCCAAACACCTCAATGTCCAAATAGCAGCCTCGGAGAAGCTGGCACAGTGTCCCCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020882-Cacnb1:NM_145121:11
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:
PF0062516=Guanylate_kin=FE(27.6=100)

							
A:
NA

							
C2:
PF0062516=Guanylate_kin=FE(17.1=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000099433





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000017552, ENSMUSP00000090412, ENSMUSP00000103186, ENSMUSP00000103187, ENSMUSP00000128095
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:39178080-39183712 
ALTERNATIVE
HsaINT0026543
(CACNB1)
Human
(hg19)
chr17:37334333-37339965 
ALTERNATIVE
HsaINT0026543
(CACNB1)
Rat
(rn6)
chr10:85958437-85962110 
LOW PSI
RnoINT0028219
(Cacnb1)
Cow
(bosTau6)
chr19:40306329-40309460 
LOW PSI
BtaINT0030527
(CACNB1)
Chicken
(galGal4)
chr27:4110745-4110833 
LOW PSI
GgaINT1008197
(CACNB1)
Chicken
(galGal3)
chr7:36963190-36965705 
LOW PSI
GgaINT0045683
(B6IDG6_CHICK)
Zebrafish
(danRer10)
chr3:16015174-16015277 
LOW PSI
DreINT0040127
(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"