Special

MmuINT0027855 @ mm9

Intron Retention

Gene
ENSMUSG00000041460 | Cacna2d4
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4 [Source:MGI Symbol;Acc:MGI:2442632]
Coordinates
chr6:119224243-119227157:+
Coord C1 exon
chr6:119224243-119224376
Coord A exon
chr6:119224377-119227079
Coord C2 exon
chr6:119227080-119227157
Length
2703 bp
Sequences
Splice sites
5' ss Seq
CGGGTGCGC
5' ss Score
6.64
3' ss Seq
TGCCCTCTCCTCCCTGGCAGCTC
3' ss Score
11.13
Exon sequences
Seq C1 exon
GCTACTACACACAGATCTCCACACTGGCGGATGCGCAGGAGAGCGTGATGGAGTACCTGCATGTGCTTAGCCGCCCCATGGTCATCAACCATGACCACGACATCATCTGGACAGAGGCTTACATGGACAGCCGG
Seq A exon
GTGCGCACGATGATGGGTCCAGATGGGCAGGGGGGCCAGAGTTAAGGGGAGGAGCAAGCGGTGACATCTTGGTCCGGAGAGTCTAACGTTGTGCCTCCATAGGAGGAGGCATCAAGTGTGACAAAAAGCCTTCTGTCACGTCCTTCCCTCACAGCCCTCAGCCTAAGCTGCAGCCTCGCTCTGTGCCCACCTGCCCCAGAGGCCTAGATCCCTGCGCAACAGACACCCTACCCCTGTGCTCCTGGTCACTCCACATTACTCTCCATACTGTCCTCTCCTGCCAGCCATGGGAAGAGAATATTCACACCAGTGGTTCACCATTCTGTAGCATGTCACAGGCTGGAAGAGGTGATATCTTGTGCAGAGGAATAAAGATATCCAAGATGGGAGGTCACGAAAGATGTTTTGGGGGATGTGAGGGAGACCTTCCTGCCTCTTCCCAGGTCGCACCTACATGTAGCCGCCTGCCTTGGGACAATAAGCAAACTAGGATTAAGACCTGACAACAGTGGCTTAGATAAGACCAAGGCAGAGAAAAAGCGTAGAGGTTTAGTGCTGGCCATCTCAGAGCTGGTAAGGCTTCTGCTCACAGGAACCCAGGCTCCTTCCTCCAGCCCAAGCCCCAACTCCCTGCTTCTCAGGGCTAGCGTAGACAATCCTGATGAGCCCCTTAAAGGAGACCACTCAGGAGTCCTCCTGGCTCACACACTTACCTCTTGCTGACCTCAAACCCGTGTTGCCTCCCAAGCTACCGAGGTGGCTGAGAAGACACCATGCCCTTTTGGCTTTTCTTTTCCTGTACTCTGTATCTGAGGACAAGGGCACATGCACTCTAGCATATAACCATAGCTATAAACCACCTTGCCAAGCTGGGACCAAAAGCCTTAGGAATCCATTCTCAAGTTCCTTCAGTGCATCTGACCTGCTGGAGCAGGCTCTTCCCGGAAGCCTTGCCCAGGGGACCCCATCTGTCACACACTGATGGCTGAGACCGCAGGGAAGAACCTTCTCCATTTGTTGTCCCCTCTATTGTCCGGGTGCCTGTTGGTCACAGGCTATCTGACCCTGGTTGGAGAAATGGGAGGGGAAAAGGGAGAGGTAAGAAGAGAGAGGCTAATGCCTGCTTTGGTACTGTCTTGACATCCCTACATTGCATGTGTACACTCATCCCTTCTTGCTTGTCCCTCCTCCATCCATCCCTGCCTCCCGCCCCCAGCCCAGCGTGTGCTCCCTGGGCCTCTCTCCCGTGTGTATATTATGGGCATGCTGGGGACCTGGTAGAAGGAAGTCTGAGAACTTGCAATTCGAGAGGAAACTGGGCTGTGGACAGTGGTGGCCACACCTAGGTAGTAGTCACACTTAGGTAGCAGGCAAGTGTGAGCCTCGCAGAGGAATTAGGAAGGAGGGGACAGTGGCAGAGATAAATAAAGCCTTGCTTCACTAAGCTACTGTGCAAATGATTTCAGGCAGTTCCTGTCAGCCCTACTGAGCTGACAGGAACTGAGTTACTCCACACTCAGCATGGCCTCCCAGGATCAGTGTTTGTCTCTGCCTGGAGATGAAGGCACAGTTTTATCTTCACTTAAGAAAAAAAGCCCTCTGTCCCCTCAGTTAAAGCCCCTGCTATCACATCTCTCCAAGCCTCCCCTTACTTATCCTCTGCATTGTGGACATCCCTGAAAACCAGGCCCATGTGCAGATGCCTGGAGCCTTCGGGTTAAGACAGTAGTTCACTGAGAGGACAGGTAACCTGTACCATGATCCAGAGCCAAGGGCACGGGGATAGCACACGCTGCCCAAGCATGGGGCGAGGCCTACAGGAGGTAGAAAAGGAGGCCCAGCCAAGGCTTGGCTGCAGCTCCCCTGAAGATGCTCCTCAAGCTTGGAGAGCCACAGCTCCTCGGGGTCCTACGAGTCTTGTGTAGCTGGGAAGATTGAACCTAGAATAAAGGAGATGCCAGTGCAGTCCATGCAGGGAGCACCTTGCTTCCCAGCTCCATGCTGAAACATTGGAGGAAGGGGAAGAGAACAGTCAAAGCTGCCACTGATCCAGGGAGGTCTAGTGTACACACAATGACCTCCAGGCGACCTGAGCAACAGGCATCTTGCATAGAGAGGTTGTTTCTGCTTGGCATCATTGTCATCTTCCTTCTAATAGAGGAACACCTGTAGGACCCTTCCGAGGCAGCAGGGGAGTCCCTTCCTGATCCTGAGTGGACAGAGCTCGGGGTCTGCCCCACGTGTGTTAGGGTGACCTGAGGCAGCCGATGCTCAGACACCCTGCCTTCAGGCCGTTGCTCCTAAACCACGTCTGTATGTCTGAGTGGCTGAAATGTCTTCCTTTCTGTTCCCTGGCCTGGGCCATGCAGTGCAACACCCTCAGGTCCACATCAGAGGCTTCTGAAAAAGCTGTGCTATGCTGTACTCTGTTTGCTGGGTTTGGGCTCATCCTTGGTCTGCCCAGATGAGACACACACTTGGCTCACACACTGCTTTTGCTGGGTGACATGAGCCTCACTAAACGCCTTTCCTCCCATCTCTCCCAGCCTTCCCCTGGCACTCTCACTAGCTCCCCTTAGCATCCCTGCCTCTCCTGCTGGTGAAGGGAGTGCTAAGTCTGGGTTCCCACACTGCTCTGAGTAACAAACCAGCAGATGCCTGAGCCCGCTCCTCCTCTGATCTCTGCCCTCTCCTCCCTGGCAG
Seq C2 exon
CTCTTCACATCAGAGGCACAGAGCCTGATGCTCCTCACCACAGTGGCCATGCCTGTCTTCAGCAAAAAGAATGAAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041460-Cacna2d4:NM_001033382:13
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:
PF137681=VWA_3=PD(2.4=8.9),PF0274313=Cache_1=PU(12.1=17.8)

							
A:
NA

							
C2:
PF0274313=Cache_1=FE(26.6=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000044660





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000044660f4238A, ENSMUSP00000133020
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:1879882-1882866 
ALTERNATIVE
HsaINT1006182
(CACNA2D4)
Human
(hg19)
chr12:1989048-1992032 
HsaINT0026508
(CACNA2D4)
Rat
(rn6)
chr4:151333674-151336219 
LOW PSI
RnoINT0028184
(Cacna2d4)
Cow
(bosTau6)
chr5:108782043-108783068 
BtaINT0030495
(CACNA2D4)
Chicken
(galGal4)
chr1:61196448-61198953 
GgaINT0120282
(CACNA2D4)
Chicken
(galGal3)
chr1:63190360-63193025 
GgaINT0120282
(CACNA2D4)
Zebrafish
(danRer10)
chr4:20555392-20556654 
DreINT0040063
(cacna2d4a)
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"