Special

MmuINT0027907 @ mm9

Intron Retention

Gene
ENSMUSG00000057914 | Cacnb2
Description
calcium channel, voltage-dependent, beta 2 subunit [Source:MGI Symbol;Acc:MGI:894644]
Coordinates
chr2:14905878-14908560:+
Coord C1 exon
chr2:14905878-14906066
Coord A exon
chr2:14906067-14907214
Coord C2 exon
chr2:14907215-14908560
Length
1148 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TGTGTGTCCCTTTGCTTCAGGGT
3' ss Score
10.94
Exon sequences
Seq C1 exon
CAGGAATCATTTGATGTGATCTTGGATGAGAACCAGCTGGAGGACGCTTGTGAGCATCTTGCCGACTATCTGGAGGCATACTGGAAGGCCACCCACCCTCCCAGCGGTAACCTCCCCAACCCTCTGCTTAGCCGGACTTTAGCCTCCTCAACTTTACCTCTGAGCCCCACCCTCGCCTCTAATTCACAG
Seq A exon
GTAAGAGCACTTCCTTTTATGGTCTTCATAGAGAATCTAGGCTGCCTCAGCCGATGCCCCTGAGACTCAGCTCCAGAGAAGAAATAGCATGCTTGATCTACTATTCTTTGCTCTCCAAACTAAAAGAGCCCAAGCGCCACTGACCAAGTTCTCTCAGTCCAGTATGAGTTGTGTACCTGTAAGCAAAGAGCTGTGAACTAACACACGACAACACCTCAGCCTGTCCTCTGCGAAGGGTCTAGAATAGTACATGTCCCATATAAATGCCCCATCTTAATGAGTTTTAATATATTCAAGCAGATTAGTTAAGACTGTGGTTATAGCCGGGCGTGGTGGTGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCCAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGATACAGAGAAACCCTGACTCTGGAAAAAAAAAAAAAAAAGACTGTGGTTAGAAGATATGGTATCAGTACTAAAATCACAAAAGACCATTCTTGCCCCTTTGGTGAAACAAAATGTCGTAGGAACACAAGTCCAATTTAAGTTGTGCCACTAGGTGTTTCTTTCATTTATTTATTTATTTATTTATTTATTTATTTGGGTATTTATTTCATTTACATTTCCAATGCTATCTCAAAAGTCCCCCACACATTCCCCCACTCACCCACGCCCACATCTTGGCCCTGGCGTTTCCCTGTGCTGGGGCATATAAAGTTTGCACGACCAATGGGCCTCTCTTTCCACTGATGGACAACTAGGCCATCTTCTGATTCATATGCAGCTAGAGACACGGGCTCCAGGGGGTACTGGTTAGTTCATATTGTTGTTCCACCTATAGGGTTGCAGACCCCTTTAGCTCCTTGGGTGCTTTCTCTAGCTCCTCCATTGGGGGCCCTGTGATCCATCCAATAGCTGACTGTGAGCATCCACTTCTGTGTTTGCTAGGCCCCGGCATAGCCTCACAAGAGACAACTCGTGTTTCAAAGGGGTGAGGTGTCTAAGCTGGGCTGGGCTTCATTTCAGCATTTTAGTACTTCAAACGGACGCACTTAAGTGATACTGCTCCCAAGATACTTAGTTCCTCAGTTGATGGCCTCCTGTGTGTCCCTTTGCTTCAG
Seq C2 exon
GGTTCTCAAGGTGATCAAAGGCCTGATCGCTCTGCTCCCCGGTCTGCTTCCCAAGCTGAAGAAGAACCTTGCCTAGAACCCGTCAAAAAATCCCAACACCGTTCCTCCTCAGCCACACACCAAAACCACCGCAGCGGGACAGGTCGAGGCCTCTCTAGGCAAGAGACGTTTGACTCTGAAACCCAAGAGAGCCGAGACTCTGCCTACGTGGAGCCAAAGGAAGATTATTCACATGAACATGTGGACCGGTATGTCCCACACCGCGAGCATAACCACAGAGAGGAGACCCACAGCAGCAATGGCCACAGACACAGGGAGTCTCGCCACCGCTCTAGGGACATGGGTCGAGACCAGGACCACAATGAGTGCATCAAACAACGAAGCCGGCATAAATCTAAGGATCGCTACTGTGACAAGGAGGGGGAAGTAATATCCAAGAGAAGGAATGAGGCTGGCGAGTGGAACAGGGATGTATACATCCGCCAATGACCGTGCGTGTCCCTACCCCCAAGTCTTTGTGTATCATCCTTAAGCAAAATCTTTGGGGGTTACATTGCAACCATATGTGATTTGTCTTGTCTATTTTGTATTGCTGTTGCTCCAATAGCAATGGCATGCAATCAAGTATTACTATACATTCTTTTGTAAGTACCACAGAAATTGGCCTAGTACAGCTGCAGACTATATCCTGAACAATTCAAAAGCTGTTTGGGTAGCTGCCATCTCAACAGAGTGGCTCCAGAAACGTAGTTACTATATCCAGTGAGCCAGATGCAGCGCAGATAACAAGTGGGATTTCTCCGTATTTTCAATACCCAGATACCTGACCTGTCATTCTTTCATGGACCACTGTTTCTTGCTTGTACCTCTGGCTGACTAAATTTGGGGATAGATTCAGTCTTGCCTTACACAAAGGGGATTATAAAGTTAGAATCTATTTTCTATGTACTAGTACTGTGTACTGTGTAGACAGTTTGTAAATGTTATTTCTGCAAACACCTTATTATAATTATATATGTATATATAATTATATATACGTATATATAATTATATATACATATATATATATATATATATATATATATATATATATATATATATCAGTTTGATCACACAATTTTAGGGTCTTAATGCCAAGTCAGCAGGTTTGCTTTATGAATCACAGGGACTAGAAATGCCCACATTCAGGAAATTTCTAATATTGTCTAGATAACTCTCCCTATTCTAAGAGAGAGACTGTACATACTGTAAATACGTGTGATTGCTTGACTTGAGGCTTGATTTATGAATGTAATCCCATCCTTGTAAGTTTTTCATTTTAACCATAAATTATGGTAAATGTAACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057914-Cacnb2:NM_023116:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.524 A=NA C2=0.988
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0062516=Guanylate_kin=PD(14.3=41.3),PF068127=ImpA-rel_N=WD(100=44.4)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000110371





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000070063, ENSMUSP00000110367, ENSMUSP00000110368
  



Associated events






Conservation


Human
(hg38)
chr10:18538366-18539229 
ALTERNATIVE
HsaINT0026558
(CACNB2)
Human
(hg19)
chr10:18827295-18828158 
ALTERNATIVE
HsaINT0026558
(CACNB2)
Rat
(rn6)
chr17:82016443-82016995 
ALTERNATIVE
RnoINT0028233
(Cacnb2)
Cow
(bosTau6)
chr13:33283701-33284611 
ALTERNATIVE
BtaINT0030540
(CACNB2)
Chicken
(galGal4)
chr2:19004340-19009039 
ALTERNATIVE
GgaINT0097897
(CACNB2)
Chicken
(galGal3)
chr2:19049669-19054365 
GgaINT0097897
(CACNB2)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TAGCCGGACTTTAGCCTCCTC

				
R: 
GTGGGTCTCCTCTCTGTGGTT

				
Band lengths: 
352-1500

			

		

	





	
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"