Special

MmuINT0085469 @ mm9

Intron Retention

Gene
ENSMUSG00000038319 | Kcnh2
Description
potassium voltage-gated channel, subfamily H (eag-related), member 2 [Source:MGI Symbol;Acc:MGI:1341722]
Coordinates
chr5:23832167-23836940:-
Coord C1 exon
chr5:23836729-23836940
Coord A exon
chr5:23832596-23836728
Coord C2 exon
chr5:23832167-23832595
Length
4133 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
CCTCGTCACCCACACCTTAGGTC
3' ss Score
7.01
Exon sequences
Seq C1 exon
GGGCCATGCACCCCCTGCGCAGTGGCCTGCTTAACTCCACCTCAGACTCTGACCTTGTACGCTACCGAACCATTAGCAAGATACCCCAAATCACTCTCAACTTTGTGGACCTCAAAGGCGACCCTTTCCTGGCTTCACCCACCAGTGACCGGGAGATTATAGCACCCAAGATAAAAGAGCGGACCCACAATGTCACCGAGAAGGTCACCCAG
Seq A exon
GTAGGTGTTCAAGGTGCTCTCTGCTCACCTGAGAGGAAGTTGGACCTGGGGAGGAGGGGCAAAGTTGGGGGTTGGAAGGCTAGTCAGAGAGGGAAGCTGTGGGGGTGGCTGGGGAAAACACCCAGCGTTGGGCTACAAGAACGGAGTTTGAGATGAGAAGGCCTGTAGAGAGACAGAGGCTGCTGGAGAGGGAGGGACGAGGCTTTTAGGATGGGCAGGTGTGGGTGACCAATAGACAGGGTACAAGGTAAAGATGAGATACTTGACAGAGACACTGTGAAGGCTGTGATGGGTGAGAGAAGGCAGCTAGAGGGACGAGGAAGATGCATCCAAGAGCTCGCTGGGGCAACAGGAGTGGGCTTCAGTTAGAAAGGACACATAAGTCAAGGTCAGGCTGGGCTTGAGTCCTGTAGGCCAGAGTGGTGTATCAGATGGGCTGGGGTGTCTGCTGTGTTCACCTAGTGTGGAGAGTGGCTGCCTTCTTTTGTGGGTGGGGAGCACTGCTAGTGGGTATAAAGCTATCAAGGGTCAGAGAAGAATAGCAGCGTTTGACTTCTGTAGCCTGTTTTGAGGGCTCCTCTGGTCCCTCTGTCCCTCCTAGCAGTGAGGTGGCTCACAAGACCACTGCCTACGCAGCCATAGCTGCTGTCCATGTTGGCAGTGGTGAGGTCTTAGCAGGGAGAATCCCTGGAGAAGAGGGGCCTGTTGTTCTTAGCTGCCCCCATCGCTGCTGCCCTGTGAGGGAGCTGCCCAGCTCTGGGCTCCCTTGGCTTGCCTTCTGGCCATACTCCCGTGCCTCTGGCTTTCTGGGTTCCAGCTGCCCCTTTGCATTGCCTCCAGAACATGACGGTCACCCTGGAGCCTTTATCTGGTTCACGCTTCTCCCTCTCTGGGTCCTACCTAGCTCTTCCCACCTGGGTGTCTGGCATCTGCCCAGTTCCTGGACCCAAAGTGCGTATGCCTTCGTTGTGTGAGTCTCTGCCTGTCCGTCTGTGGACTGCCTGAGGTGCCCCTGCCAGTCACCTGGCGTCTCTCCATCTCTGGGTGTCTCTGCCTGACTGTGGCTGGCTCGGCACTGGACTGGCGGGGCGGGGGTGTTGGGGAGACCATTAATCTGCGGTGACAGGCCAGGCTGCCGGGTGGAGGGGGAGGGGCTAGGGCTGCGGGAGCGGCTGCAGCAGGAACCTAGAGCGGGCTGCAAGGGAGGGGGCCCGCTGGCCAGGCACGGGGCAGAGGGCGGGCACGGGCTGGGCGGGGGGAGGGGAGGCAGAGTGGTGGAGTCGGGGTGGGAACCTGGCAGGAGGAGGGGCTGGCCAGCAGAGGAGCTGCGGTTCCCACCGCGGGTGCTGGGCTGGCGGCAGGCGGGCAGAGCACAGCACCCTGGTAGTGGGGGGCCCACACCAAGGGGCCATGTGCAGCAAGAGCCAAGCAGGCAGCTGTCCATACTCACTGCCTAGGTGACCCCAGCCCCAGGGCCCAGCCCCAGCCATTCTGGCTTCATGCCAGAGGCAGTTCTGGCTGCCAGTCGGCCAGCCTTGGGCTGGCAGCCTGGGCTGGGACTGCTGCTGGGGCACAAGTGAGGCCCTGGCCGGGCCCTGGGGCCTTAGGCCAATCAGGCTTGGGGGAGCTAAGTCCTCCATGGCGATTCCAGCCGGGAAGGAGAGCAGGACAGGGGCTCTGCAGCCCAGGGCCCAGAAAGGCCGGGTGAGGCGGGCAGTGCGCATCTCCAGCCTGGTGGCCCAGGAGGTAGGTGATTCCCTCAGCACCCTATTCTTTTCTTGGGTTGGGACACTGAGGCAGGTGGGAGTATGGCCCAGAGGGCTCTGGCTGCAGTTGGGGAGAGGGCTTCTGAGAAGCAGGACAGGTTGGGAGTTCTTCGGTGTGGCCCACCGCTGAGCTCCTCATTGCTCTCCTCCTGGCTGCTGGCTAGGTTCCCGGGGTTTCCCTTGCCTTGGCAACCCCTTTGCTATGGCTCCTATGGCCCACAGTCTTCTAGTTTAGAAGGTGAAGAAAGAAATGCTAGGAAGCAGTTAGGTGTCCAGAGAGGATGATGGGGAGATGGAGAGAGTCAGGAACCAGTAGGCAGCAGCTAGACCTGACACAGAGGTGCTGGGGCTCCCTCACTCTGACACTGTGGTCAGCAGTGGAGGCTTGGATTACTCTTGTGGGTCTCAGGGGAGAAGGGATCAGAGCTGCTCAATGGGCAATGAGGGCAGACTGAAATGAAGCATTGGGTCACCTCTTTAGGGCATCCTGGACCCCTGTCCCATCAGCTGGTGGTTGCCTCTCTACCCCACTGGCTCTCCTGCTTTAGAACCTGGAGGTAGCTCTGGGTGATTCTGAGAATCCCACCCCTGCCAACATCACTGTCCCTGACTCCCTCTGTTTGCTCCTCCCAGTGGGGGAACAGACACAGGTGAGAGTTTTCCCTTCCAAGGTGAAGATTCAAGGTTGAGTCAGTCTTCTGTAAAACAGCAAATCACAGGGGATTATAGACCTGGCCTAGAGCCATGCGGTAAGTCAGTGGTTTCAGAGATAGGACTGGCCCTTGGGTAGATTGAATTAGCAGGTTTGGGCCTTGTATCCCAGACTTGCTGGATATTTGAATGCAAATGTGCACTGGGGCTGTGGGCAGACTTGGTGGAAAGGGTCACTGCTGTCTGTGGTGGTCCAGTATAGCTCCTCAGGCCTGTGCTCAGGCACAGAGATGGGTCCTATGGAGTAACAGCCACCCCCCTGTTGCCCCTTGTCTGTGGGGTCCTAGCCTGCTCTTTTTTGATGGCTTGAAAGGTCACTAACCTCGTGTATTAGCCCTGTGTTTTAATTAAGAAGCCCTCAGTCTGAAGGCAGGGTAGACCTAGGATCCTCCTCCGACCAGGGCCTGGTACTCATCCACACCCCATCTCTTTTCTTGGAAGTCTCTGTGTCTATTCTGGGGGGGGGGTCCTTAAGATCCATCTTTCTTACCAGCTCCTTTCCCTAAGATGGTCTCTAAACAGCACCACCTATGCAGACAGGCTCAAGGGATTCCCACTTGAACGTGAACGAGACTCTTTAGGACTTCACTGAGCCCAGAGACCTGTGGTTATGGAGCCTGGGACTCAGGACTTCTGGGACAGGGCTAAAAACTCTGGGGTTGGGGAAGGCTTCGGGTCTTGCTGCAGGCATGGAATGGTCAAGGCTAGAGGGGCTGAGGAAGGGATTCTAGCTGACTCAGAGGTCTGCCAGAGAATTCTCAGGGTGGGTGGGCAGGGGGCCTTCTGACACCCGGGAAAGCTAGTTCTCCCCAGGCAGGTTTGAGAGCAAGATTGCTGGCTGTGCTGTTGCCCCTGGTCCCTATGGTGGGCTGCCTTTGCCTGGATGCTGAGGGGCTTGTGTCCCCCATCTGAAAATGGGGTTCCGTGTAGGCCAAGAGTGCATCTCTGAGCCATCCTGGGTATATCCCTCTGTATTTTTGAGGTGCCTGGGTTGGACTCTGTCCCTTGTGTCCCTTTGTAAGAGCATGGGAGGCTAATCTGGGTTAAGGTGGAGAGAAGCCTGAGAAAGAATAGCAGCAGGGAGAGGGTTTCTCCCCTTAGGGAGGCAAAGGGGCCTGAGAATGGTGGCTGGCGTCCCTGGACAAGTGGTCTGAAGTGAGGGAGTGGCAAGGACTATTTTATGTGTTGGAACTCTGGGCTCACTGCCCAGCTGGGAACTGCAGTCCTTGGAACATATTCTAGACTGAGATGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGCTTTTGGGGCCGTGGGGCAAGATTGTATGGTGAGAGTTGCATTGTGCAATCTGAGGATCTAGACTGTCTTGTGGTGGAAACAATATTGGGCCTTCCTGCATGATGACCCAAGTTCATGTATTTTGGGTACTGTCAGCTGGTATGTCCCCCTGCTGGCTAGCATTCTGGGAACTGGAGTACCTCGGTTTGGGGAAGTCAGTTCTATGGCTACTTGGCTGAAGGTGAGCATTCTGATAGGAATATGTACTACTCGGCCATATATGGACAGTACCAACTTTTGCTCCGAAGTCCCATGACCCTTCCTCGTCACCCACACCTTAG
Seq C2 exon
GTCCTGTCCTTGGGAGCAGATGTGCTGCCTGAGTATAAGCTGCAGGCCCCAAGAATCCACCGCTGGACCATCCTCCACTACAGCCCCTTCAAGGCGGTGTGGGACTGGCTCATCCTGCTGCTGGTCATCTACACGGCAGTCTTCACACCGTACTCGGCCGCCTTCCTGCTGAAGGAGACTGAAGATGGGTCCCAAGCCCCTGACTGTGGCTACGCCTGCCAGCCCCTGGCTGTAGTGGACCTCATCGTGGACATCATGTTCATTGTGGACATCCTTATCAATTTCCGTACCACCTATGTTAATGCCAACGAGGAGGTGGTTAGCCATCCTGGCCGCATTGCTGTGCACTACTTCAAGGGCTGGTTTCTCATTGACATGGTGGCTGCCATCCCCTTCGACCTGCTCATCTTTGGCTCTGGCTCCGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038319-Kcnh2:NM_013569:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.169 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF084125=Ion_trans_N=WD(100=36.4),PF0052026=Ion_trans=PU(31.6=45.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047705





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:150952854-150957290 
LOW PSI
HsaINT0084308
(KCNH2)
Human
(hg19)
chr7:150649942-150654378 
LOW PSI
HsaINT0084308
(KCNH2)
Rat
(rn6)
chr4:7375944-7380216 
LOW PSI
RnoINT0077731
(Kcnh2)
Cow
(bosTau6)
chr4:114333087-114337699 
LOW PSI
BtaINT0079557
(KCNH2)
Chicken
(galGal4)
chrUn_AADN03018816:874-1089 
GgaINT1015895
(KCNH2)
Chicken
(galGal3)
chr27:2597890-2601834 
LOW PSI
GgaINT0142993
(KCNH6)
Zebrafish
(danRer10)
chr3:31610571-31610617 
DreINT0084785
(kcnh2a)
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"