Special

MmuINT0027935 @ mm9

Intron Retention

Gene
ENSMUSG00000017412 | Cacnb4
Description
calcium channel, voltage-dependent, beta 4 subunit [Source:MGI Symbol;Acc:MGI:103301]
Coordinates
chr2:52330383-52333331:-
Coord C1 exon
chr2:52333212-52333331
Coord A exon
chr2:52330506-52333211
Coord C2 exon
chr2:52330383-52330505
Length
2706 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACT
5' ss Score
6.64
3' ss Seq
TTCTGTACTTCTGTCTCCAGTCC
3' ss Score
8.32
Exon sequences
Seq C1 exon
GGGTCAGCAGATTCCTATACAAGCAGGCCATCGGACTCCGATGTCTCCTTGGAAGAGGACCGGGAAGCGATCCGGCAAGAGCGAGAACAGCAAGCAGCTATCCAGCTTGAGAGAGCGAAG
Seq A exon
GTGACTTTCTTCCTTTTCTTTTAACGCGAGCTGTCACGTTGCTCAGCGCCTGTGCCCAGCATTTCTACCTCACATCTGTCTTAGTGTTCCTGATAAAACACTGACCAAAAGCAACTTGGAGAGGAATGGCTTCATTAGACAGCTCTGGTCACACTCATCAGTGACAGAGTCCAGAGTAGGAACTCAAGCAGTACAAGAACCCAGAGGCAGGGACTGAAGTGGGAGCTACGGAGAAACTCTGCTTATTTGGCTAGCTCTCCACGGTATACTTAGCCTTCTTTCTGATACCACTCAGGGCCACCTGACTAAGGGCTAGACTGCTCACGGTGGGGTGAGCACTTCTACATCAATCACTGGTCGGGAGAATGTTCCCCGGGCCTGCCTACAGGCTGATTTGGTAGTAGCATGTTTGTAATGGACATTCCTTCTTTACAAACGACTCTAGCTTACGTCATGTGTCTCTCTGGAGTATTCATTTTCCAGCCATCCGGCTAAGGCTTCTGATTGCAAGGCTCTCTGTTGTTTGTGCCCCTCACAGAAGTTAGTGGTATCTACAGGAGCCTATTTCTTATGAACCTTTTGCCTTTTTCTGTTTGATTTCGTGGTAATTATTGGTCCTTTCCCAACCTAGCAGTGTGGCAATATCAAATGACCTCACAACGTATTGGCAGAGAACCTTCTGAGCGGCGAGCCTGAGCCCTCTGTTCTTGACTCCTCCCCATCCTTGCTTGCCTCTGTTACACACCCACCCCCACCATGCTACGGATCACTTCACTGCTGCTTCTGTTCTGTGGTTTCTAGATTTCAGACTCCCACTTCAACTTCAGCATGGAGTTATTTTGTCTGCCTGTTTGTTTGAGAAGGGGACCACTACACTGTCCATTCTGGTCTTGAACTTGTGGACTTACTAGCTGGGCTACAGATGCGCACCATCGGACCTGGTTAAGCCCTTTGAACAACTCAAACAAGAGCAGCAAGACAGAGTGACAGAAGCCATCACTAGCCAATATAGGCTTCAGATCTTCTTCTTCCAGAAGACACAGGATGCAGCAGGAAACCAGCTGCACAGTTGAATTTTAGGACCAGAATTGCTACTAGAGCTCTCCCATTCCTCCTATATCTTTCTAACTTATTTTTCAAAGCATAGATAGGCCCTTTTGGCAAATTAATTTTTATGCCCAGCAACAGCATATGAGACACGGTTTATGGCTAGCCTGTCTGCTTGCTTCCATAGCTAACTCCAGTTTAGAATTTTAGACTCAAGCCCAGATAACGTTAATTTCCTTCCCTTTCTGGTTTCTGATAAGCTGCTTTAGAGATTGAAGCAAGAGAAGAAGGATATGGATGGGTGCATCATTGGGGTTGAGTGTGGGGTTGACGTCCACACACTGTGTCTGTGATCTCTGGTAGGAGGGCATCAGCATAGTGCCTGGGAGGGGACAAAGAGGTCCTACTGTGTGTCCTACCTCAACTGTTGATATTCCCAGAGCAAATGAATAAACCCATAGCAAAGCTACCTAGAGGCTTGGAGACCTTGTTGCTTGTTCTTGTTTTGAAAATGTCCCTTGCCATCTGTTTCATTATTGCGTGGTCACCTAAAACGGGGGTGGCAGGACCATAGCCTCGGCTGGTGGCTGGCTTAGCCCCAACAGGCTGCACCTGCTCAGGAGCACTTTGCCAGCAGGAATTCATATGCAAATTTAAAACAACCAACTGTTAGAAGGTAGGAAGAGGGTACAGGTGAAGAGCCTGTGTGTTGGGTTTAACCTACGTTGGCCTCCATTCCCCTGGCATGACAAGATGGTTATCTACAAAAGATCTCAGGTTTTCAGAACTGAGGCTCTTTCAAAAATCCTTGTCTTCCACCTACCCACCCTCCCTCAAGTTTATAACACCCAAGGTACATTTCCTAGCATGTTTTTCTTCTATGTGTAGACTTGCTCCTCTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCGCACTCGCAAGTGCTCCCATGAGTACACATATGCATAATTATGCACATGTGTGTGGATGTCAGAGGTTAATGTGTTTCCTAATCACCCTCCATCTTAATATTTGAGGCAGGTCTCTTACTGAACCTGGAGTTCACCTTTTGTCTAGACTGGCTTGGGTCAGCAAGTGCCAGAAATCCTCCTGTCTCTGCCTCCCCAGAACTGGAATTAAAGATGCACAGCTCTGCAGCCCGCTTTTGTCACAGATACTGGGACTCTGAATTCAGTTCCTCGTGCTTGAGCATCAAGTACTTCAACAACAGAGCTGTCTTCTAGAACTTCCCTCCCCCAAGTAGACACGTCCTGTATCCCACAGTTGGGACAGTGTCTGGGACAGGTTAAAGTAAATCCACAGCTTGTAGGAGCAGAGAGAGCCGAGCTGACTGCCCCACCTCTGTACATCCCTCCCCTGTCTTTTTGGGGCTGGCTCCTTATTGAGGATGTTAGGAAGTACTGCAGAAAGAAAATGGCTGGGCCGAGAGCAATGAGTCACTCCCGGAGTCATCTCTGCAGATCTCGGGATGTGGCCTGCAACTATAAAACCCAGAGGAGAGCTCTCTCTGGAAAGTGATTTCCTTGTTGCCTGGAACCATCATTCATCCTGTGACATGTTTCTATAGGAAAAATGCTTCTCTCTCCCGTTCTCTCCCTCGCTCACTCCTCATTCTGTACTTCTGTCTCCAG
Seq C2 exon
TCCAAACCTGTAGCTTTTGCGGTGAAAACGAACGTGAGCTACTGTGGTGCCCTGGACGAAGATGTGCCCGTTCCCAGCACAGCCATCTCCTTTGACGCCAAGGACTTTCTTCACATTAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000017412-Cacnb4:NM_001037099:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.867 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF120523=VGCC_beta4Aa_N=PU(92.9=97.5)

							
A:
NA

							
C2:
PF120523=VGCC_beta4Aa_N=PD(2.4=2.4),PF0001823=SH3_1=PU(44.2=46.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000077438





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000099821, ENSMUSP00000099822
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:151880923-151883250 
LOW PSI
HsaINT0026593
(CACNB4)
Human
(hg19)
chr2:152737437-152739764 
LOW PSI
HsaINT0026593
(CACNB4)
Rat
(rn6)
chr3:37997560-38000152 
LOW PSI
RnoINT0028258
(Cacnb4)
Cow
(bosTau6)
chr2:44401137-44403445 
LOW PSI
BtaINT0030567
(CACNB4)
Chicken
(galGal4)
chr7:34852679-34853020 
ALTERNATIVE
GgaINT0045675
(CACNB4)
Chicken
(galGal3)
chr7:36977521-36977862 
LOW PSI
GgaINT0045675
(B6IDG6_CHICK)
Zebrafish
(danRer10)
chr9:38301691-38301812 
LOW PSI
DreINT0040185
(cacnb4a)
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"