Special

MmuINT0027911 @ mm9

Intron Retention

Gene
ENSMUSG00000057914 | Cacnb2
Description
calcium channel, voltage-dependent, beta 2 subunit [Source:MGI Symbol;Acc:MGI:894644]
Coordinates
chr2:14882282-14885609:+
Coord C1 exon
chr2:14882282-14882418
Coord A exon
chr2:14882419-14885532
Coord C2 exon
chr2:14885533-14885609
Length
3114 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
GAATGTTTGGTTTCCTTCAGTAA
3' ss Score
5.75
Exon sequences
Seq C1 exon
AAATTTAATAATGACTGGTGGATAGGACGGCTGGTTAAAGAAGGCTGTGAAATCGGATTTATTCCAAGCCCAGTCAAACTAGAGAACATGAGGCTACAGCACGAACAGAGAGCCAAGCAAGGGAAATTCTATTCCAG
Seq A exon
GTATGAACAACAACAACAACAACAAATCACTGTTTATATAAAAATGCAGACGTTGTCCTCGCTTCTGTCCTGTTGCTTGCTGAGTGCTGTGATCCTTAGTGTATACTGAGCAGATGCTGATGGTGTTCATAGAGAGCATCACCGTTCCTTTTAAAAACACTTCACTCCAGCTTCTGATTCTAATTGAGAATCAATTGATTATGATCATTAATAAAAATAGCTATGGTTACAAAGCACTACATTTTGCCTTCAGCACAGAGGAGACCCTGAAATCCTAATCATTGGCTGAACATAGGCAAGCAGCAACCACAGTGACTAATCCCAGTGTCTGTCTGTAGCTGCCCAATGTGGCTGACAGATGCTTGAGGGATATCAGCCTCAGGCATCACTGACAAAGAGCAGCTCCTGTGGTCTCTTAGTTTCATTTTCACTTGAGAGATCCAATTTTCAATTCTACCAACTGTTAAGCACAGAAAAAGACACCATGTATGAAGCAAAATTGCCTTCATGAATAGCAGTTAGCTGAAGTTATGCAATAGGCTAGATCTATTACTCTGATAAGACCTTCTTAGGAGGCTTACTCTAGGCTTCCCTTCAGCAAGACATTCATTAAGAGGGCTTCTCACCCAGGAGGCGAACTTCATACTGAAGCCTGTGTATCCAAGGTGAAGAATGCAGTATGCTTCTCACATGGATGGAAGGAGAAAGATGGGAAGACTTTATCTTCCTGTGGGTGGCTGAGTTTCAGTCTTACTCCATTACAACTTGCTTGTTTGTATAATGTCAACTCCATTGTTAGTGCTTAAAATTTTAATGTTAGGAAGTATTTTTTACCTACTGTCATGAGATGAGTGAAACTGAATGGCTGTTGCCTCATTAAAACCAGAACTTGATCACTGTCACACTCCTACTGTCTTGCAATTTATTCTACAGAGCTGGGTTACTTCCTCTTCGAACTGTATAATGTTTCTTTGACTTTCATGATTTTATTTCATTGCATCTGTCTACCAAACTTTTATCTAGGTATGCCTAAGGACATCCACTCTCTTCCACAAGTATTTACATTTGCCTTTCGACACTTTTATATATTTTGTAAGGACATAATCAAAGTCAGTGTGTATGTCTATGTGTATATACATACAGACACACACACATATATACATACATATATATGTATATATAGTATACATATATATAACACATATTTCAGAAGGCTGAATTTTATGTAAATATGCATATATATTTATCTGTATTATATACACACATATGTATGTGTATTTATATACACATATATATATATACATACATATATACACATACAGAAAAATTTCAAAGACTGACAAAAGTCAGGAGCTAGAGAGATGCCTCTACAGTTAAGTAATGTCATGGTGCTCTTCCAGAGAACACAGGTTCAGTTCCCAATACCCACATGGAGTCTAACACTTGTCTGTAACCTTAGTTCCAGGGATCAGATGCCCTGTTCAGGCCTCCATGGACATTGCACACAGGTGATCCATTTACATATATGTAGGCAAAACACTCATGTATAAGAATAAAAATGTTTAAAAAGACTAACAAACATCAAAGGCACAGAGCACAGTTCAAGAACTTGGCATGTGGATGTCACATCATCCTCTGAATGTTTTACGTATTAGCGGCATCTGTCACAATTTTACACAACATAGTATACTGCCTATTAAAACTAATAAACCAGAAGAGCAAACCTGTGCTTGATCTAAAGTTAGGCTTTGGAGTTTAGGAGGCATACAAACAAAAGATGAAAGCTGCAAGAAAGAGGTGCTTGGTCTTAGCAACAAGCATCCTCGCACATTTCCCAAAAGTGATTCCATAAGCTCCACTTTTTACTAGCTGTATACACTCCTTCATGTCCTTATTGGGTGAGCGGGTGAGCAGGATTTAAACTTTAGGGATACGCAGAGCTCACCTGCTGGTTGTTTAGTAAAGTGATTGTCCTTTGCTTTGTGTATTAAAATGCTAGAAGAGTAGGAAAAAAAAATCAACCAGCAAGGGCAGAACTTTTAACTGCACATCAGTATTTAGCTAGGGCAGCAGTGCCTCTTGAGGCACACACATGGTACATGGTTCTTCCTAGTAGAACCTGGATCATCCATGATAAGATGCACAGGTTGGTGCAGTTATATTGCTTGAATTCCATGACATTCATATTCAGATAGCGTATTTCTGGGTTTTATGTGTTAAGGGATGGCACGCGTTCCTCTATCCTAGTGAACCACCCATTCTATCAACTCCAACATTTCTCAAACACACAAGCATATGCTCCATCACACTTATGTCTGGTAACTGAGAAGGATTTTTAAACTTTGATTTTTTTTAATTCTTTTTACATTTAAAACTAGCATACAATATATTAGATGCCATTATGACACTTTCTTATAAAGCATGTTTTAGTGGATTCTCCTTTGCCCCGTTCAGAAGTGTTGAATAATCTTCACAACTTAACCAAGTGGAGTCCTTCTTGTTAAGCTTGTTTTGAAAATGTTCACTATTGTCTTCTGGTTAATTCATATTGTAATCCTTGTTTGAGTTTATTCTTGTGTCTTAAAGATTGGTGAATCGGGACACTGCTTTGTTCCAATTGTTTATCTTTTGCAGGTTACCATGAAAGCTGTACTTTTAATCTTAAGCTACTAAAAATAATCAAGCTAATCCAAAGGAACTGGATCTAAGTGAGGACACATGAATTTTAGGTGTTAGCATTGAGGCCATACTCTTTACCTCCACATCCTCTAAATGTAAAGGCAACGCATGTCTTCCCTGTCTGCCTATCTAAGATCTAGTCATGGAACTTGAGAACCAGAGAAATTCTCCTAGCTCTTTCCCATACCCTCAGGAGCATAAAGAAAAAAAAAAAACACACCCTAAATTTCAAAACAGAAACTATCATAAAACTGTTTCAAGTACCACCGGAGTCTCCACTGGTTAATGACTGCTTGCTTCCTTTAAACAAATACACATTTTTCAAGAGTTCAATTAAAAACATAATTTATTCATTATTACATTTATCCAGAAGTACAATGTTTTTGTGTCTGAAACGACTGTTGCCTTTAAATCTGAATGTTTGGTTTCCTTCAG
Seq C2 exon
TAAATCAGGAGGGAATTCATCATCCAGTTTGGGTGACATAGTGCCCAGTTCCAGAAAATCGACACCGCCGTCATCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057914-Cacnb2:NM_023116:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.351 A=NA C2=0.837
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0001823=SH3_1=PD(44.9=47.8)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000115262





     
                   









    
Main Skipping Isoform:
ENSMUSP00000110371





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000070063, ENSMUSP00000110366, ENSMUSP00000110367, ENSMUSP00000110368
  



Associated events






Conservation


Human
(hg38)
chr10:18500949-18506470 
ALTERNATIVE
HsaINT0026561
(CACNB2)
Human
(hg19)
chr10:18789878-18795399 
ALTERNATIVE
HsaINT0026561
(CACNB2)
Rat
(rn6)
chr17:81992445-81995424 
ALTERNATIVE
RnoINT0028236
(Cacnb2)
Cow
(bosTau6)
chr13:33244401-33247401 
LOW PSI
BtaINT0030543
(CACNB2)
Chicken
(galGal4)
chr2:19029339-19031005 
ALTERNATIVE
GgaINT0097889
(CACNB2)
Chicken
(galGal3)
chr2:19075330-19076997 
LOW PSI
GgaINT0097889
(CACNB2)
Zebrafish
(danRer10)
chr7:71625336-71626476 
DreINT0040140
(cacnb2a)
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"