Special

MmuINT0027881 @ mm9

Intron Retention

Gene
ENSMUSG00000041460 | Cacna2d4
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4 [Source:MGI Symbol;Acc:MGI:2442632]
Coordinates
chr6:119299113-119302425:+
Coord C1 exon
chr6:119299113-119299195
Coord A exon
chr6:119299196-119300048
Coord C2 exon
chr6:119300049-119302425
Length
853 bp
Sequences
Splice sites
5' ss Seq
GAGGTGCGG
5' ss Score
6.79
3' ss Seq
TTACCCCTCTGGCTTTTTAGGAG
3' ss Score
10.36
Exon sequences
Seq C1 exon
ATAATGCCTCTGTCAAGTGTGACAGGATGCGCTCCCAGAAGCCCCGGAGACGACCAGGCTCCTGCCATGCCTTCCATCCAGAG
Seq A exon
GTGCGGGCTATGAACTAAGAGGCTTGGCCTTTGACCCCTAGTTTTGTCCTGTGTGTGGCTTCTTGGGACATGAGTATTTCTGGACTATGTGTCTATCATGCTGGGGGAGCCCTGCATCCACAATGATGTTGTGTGATACACAGAATAAGGAGCAGTGGCAAGCAAGGATGTTCCAGGTCAGTTGGGGGAGGGGGAGGGGCAAAGGAAAGCAGACAGAGAGAAAGGGAAAAGGACCCAAGGGCATCTGTACTTCTAGGGCCTGGAGCCCAGTAAGCTTCCCCTCACATCCTTCCTGACTTCTGAGACACCTCAGCGCTACTTACCATGACTTAGCTAATGACAATAGCGACTGGTATCTATTAACCCCTAAGCCAGGGACCTTACTACCCAGTCTCTGCTGGGTGTGGCTGCCTTTACAAACTACCTCCCTAGAGGGGCTCCTGGAGATGACAGCTGTTCCACACAATTATGAGAGGAAGGCCCTAAAGATTTAAGCAAGTAGTCTCTACTGTCCCTAGAAGATTGAAGAAAGGCAGGTTTCTTCTCATCTTTGAAACCTCGCCGAGCCAGGCGTGGTGGCGCACATCTTTAATCCCAGCACTGGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCAAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTGGGGCGCGGGGGGGGGGGGGGGGGAGAATCTGAAACCTCGCCATCTCCAGGCGAGGCTGGAAGCAGGCTCTTATTTTGTCTGTGTGCACCCATGCTGTACATGCCAGACCTTGGCCACCTCTCTCCTAATGCTCCTTACCCCTCTGGCTTTTTAG
Seq C2 exon
GAGAATGCCCAGGACTGTGGCGGTGCTTCAGACACTCTGCCTTCATCCCCTCTGCTCCTGCTATCACTGGGGGCCTGGCTGCTTCCACCCCAGCTTCTGTGGTGACTCCATCCCATCTGACTTTCGCAGAAGGGGGACCTTACAGGACATTCTACAAAGTTACCGGCTTATGAAGGCCCCTCACTGCTGTGGGATGTCTCCTGTTTCAGTCCTGGGGCTACAAGTCTCTGCTTCTTAGAGATTGCTAGAGGGATCTCCAAGGCTCTTCAAGTCTTCTACTCTTGTCTCAAGTGAAGGAAGGACAGAAGTTCATTACTCCAGTTTACCAAAGGGTCACCCATTTCCCTGGCTGATCTGCTGATCCGAGGAGTTCTGGAGGCTGGAATTGAGCGGCGAGGCCCATGTAGAGGCTGTGGCAAGAGTGTGCTTGCCACCAAAGGGAAGGTGCTTTTATCCATCAGATAGTGCAGAGGACAGGCAGAGGGAGAGACAAAAGACTAGGGAAGGGACCAGAAGAGGAGGGAAGAAATGGAAAGGAAGCTGGGCGTGGTGGTTCACACTTTCAATCCCAGCACAAACGGAAACAATAGGAACGCAATGGATATTAAGTCCTGCGAGCTGTCATTAGCTACCTCTGAAGAGTCTCAACCTTTTTACACTAATGATCTGGAGAGCGGGCAGGGGTGTATGGGAGGAGGTGGAGGGGAAGGGAAGGGATAAATGCTGTAATTATAATCTCAGAAAGGGAAAGAAAAGCTTTTAGGATGAGCTCTGCAGCTGCTGCACTGGGCCAAGCACCAGTGTGGCACTGGACAGGCATGATCCTGAGGAGGTGGCGAGAAAAAGCAGAACCGAGACTCGCGCCTCACAGACTAAAGGAAGGAGCCAGGTGAGGTCTCCAAGAGCCATAGTGGGCTTTCTGTGGCTCACAATGTACAAAAGAAACCAGACTGTTGCTGGGGAAAGTCCTGGAGGCTGGAAACAACACATAATCATTGCCACAATGCCCAAGTGAACACACACACACGCCCGTGCGCACACATTTGTGTACCTGTTTGTACAAAGATGTGGAGGCCAAAGGTAATATTGGCCGTTTTCCTCAATTACTCCTTTAATTTTTTTTTTAGATAAGATCTCTCACAAAATCTGAGTCCTCCAATTCATAGCTGGCCAGCAAGCCCCAGAAGCCCTTCTGTCACTGTCTCCCCAAGGCTGGGACTGCAAGCATGCCCCGCTGTAGCCCTACTGTTGGAATAGTTCAGGAACCTAACTTGGGCCCTCATTCTCCACTAGCTGAACCTCTCAAGCCCCGCGTATCTATCTTTTAAATCAGGAACCTAAACTGGCAGCCGTGGTGCACGCCTTGAATCCCAGGACTGGGAGGCAGAGGGAGGAAGATCTCTAAGTATGAGGCTAGCCTGGTCTATAAAATGACAGACACCCAGGGCTACACAGAAACCTTATCTTGAAGATAAAAAAATAAATAGAAAAAGAATAAAAGCTAAAACTTGGAGAAGGGAAACTGGTTCTAAGTCTCGGCTTTGTGTAGTAGGAGGCAATGTACCTAGCACCAGCTAGCACTCAGTAAGCACTAACAGCACACTAGCTAGCATCCTGCATCGGGGATTGGAACGTAGGGAAGGTCAGAGGTGCTGCCAGGTGAAGTACCAAACTGTTATAGCAGTGTTTTCTCTGTCAGGCACGGCAGGTCTTTCCTGACCACCGTCACATCACCTGCCTTGTCATCAGTGTTATGACCTCCTTTCAGCAGCGTCAGGTCTCAATGGCAAGCAGGCAAGTCTCTTAAAGGACTTGTCTCCTTCACCCAACCAGGCAGAACATTTGGGGACGTTGATCAACTCTTTAGGCCACTGGAGAAATGCTAAATGTAGGGTGCCAGGCAGCTCCTGGTCAGGAGCCACGGGGCTCTCGTGCCTGGCACTGAGGAATCGTTTAGAACACCACCAGAGCAGCTGAAGAGAAGGCATTTCATGATGCTCTGTCCCTACCATGGACACCAGGTATCTCCCAAGGTGTGCCTGCCTCTCAATTCTGAGACTAGTGCCGCCAAAGGACATGTAGGAGGATGGCCAAGACATGACGTGGCAAGCTAAGCCCTCCTCAGTGAGTGATCATAACTCCACCAAGACACTGGAAGACTGCAGTCTGGATTAGGTGAAAGATCTGGCACCTTGACTTTAGAGGAATGAAGTTGGCACCCCCGAGATTAAATGAATGGAATGCAGCATTCTGGCATCTTTCCTTATCTGTGTTGCCTTCAACCACAAGAGCTGGAGCCCTGTCAGAAGCACCAGGAATGTGCCGCTGAGCTTATGTGCTAGAGTAGAACCACCTCAAATAAAAGGCTTCAACAGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041460-Cacna2d4:NM_001033382:37
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.286 A=NA C2=0.118
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000044660





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000133020
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:1793760-1795298 
ALTERNATIVE
HsaINT0026534
(CACNA2D4)
Human
(hg19)
chr12:1902926-1904464 
ALTERNATIVE
HsaINT0026534
(CACNA2D4)
Rat
(rn6)
chr4:151408479-151409158 
ALTERNATIVE
RnoINT0028210
(Cacna2d4)
Cow
(bosTau6)
chr5:108731431-108732033 
BtaINT0030520
(CACNA2D4)
Chicken
(galGal4)
chr1:61114020-61115041 
ALTERNATIVE
GgaINT0120306
(CACNA2D4)
Chicken
(galGal3)
chr1:63107223-63108244 
ALTERNATIVE
GgaINT0120306
(CACNA2D4)
Zebrafish
(danRer10)
chr25:18925879-18928911 
LOW PSI
DreINT0040118
(cacna2d4b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TCAAGTGTGACAGGATGCGC

				
R: 
CTTGAAGAGCCTTGGAGATCCC

				
Band lengths: 
342-1195

			

		

	





	
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"