Special

MmuINT0085520 @ mm9

Intron Retention

Gene
ENSMUSG00000001901 | Kcnh6
Description
potassium voltage-gated channel, subfamily H (eag-related), member 6 [Source:MGI Symbol;Acc:MGI:2684139]
Coordinates
chr11:105875699-105878974:+
Coord C1 exon
chr11:105875699-105875904
Coord A exon
chr11:105875905-105878548
Coord C2 exon
chr11:105878549-105878974
Length
2644 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
ACCCATGGCTTCCATCCCAGGTC
3' ss Score
7.38
Exon sequences
Seq C1 exon
AGGGCTCTCACAGCAGGCCAAGCGGACAGGGGCCTGGTCCAGGCAGGGGCAAGTATGGAACTGTCAGCCAGATCCCGCAGTTCACGCTCAGCTTTGTGGAGTTCAACCTGGAGAAGCACCGCTCAGGCTCCACCACAGAGATTGAGATCATCGCTCCCCACAAGGTGGTGGAGCGGACACAGAATGTCACTGAAAAGGTCACGCAG
Seq A exon
GTATGGGTCTGCAGGAGAGCGGTGAGGGTGGGCGGGGTCAGAACCCCTGGGTCCCTTGGACCTCAGCTCTTTTAAGGTCATAACTAAGAAGGGAGATGTGACTTGTCCAACCTCTCCCTGCCCCCCACCTCACATCTTGGTCTGAGTCCCCAGCCTCGTCTTCTATAGTTTGAGTCAGATTCTTAAGACCTGAAGGCCTGGTCTGAGGCCACAGCCCTGAGGCCTGAAATCAGCAGAGGTTGGGGTGAGCAAGGCCTATGAGTACTTCCGAGGCCTGGAGATCCCAGAAGGATAGGAGGAGAAAACACACAGGCCACCTTGGGGCCAGCCTATGGTTCTGCAGTCACAAGGCAGGAGTGGTACAGAGGGTCAAGCCCATGCAAAGATGAGGAGAGGAAGGAGGGATGGGATGAGCCCTGCCCTGGTCCTGCTCCTTCCCTCTGCTTTTGGGACGATGGCCACTCCTTGCGTTGTATGCAAACAGTACACCTGGCAGGAGTGGGGTAGTGTCGGTGTCTCTAGCTAACTTTGGATCCTGGGGATCCATCTCTAAATGCCCCTCCTGTGCATCTTCTATTTGGCACATGTCCCTTACTGGGTCCTGGGTTTCATCTGACCCCGACAGTCCCTTCTAAGGGGCTTGTTGGCCTGATTCTTCCAGGGGCAATTGACTAGAACCCTGCTTGAGACTGGAGTCAATAGGATGCTGGCACTGGCACACTATGTGACCTTGACAAAGGACACCCCTACCTTTGGGCCTCAGAGCTCTCATATGCAGGAAAGAGTTAGGCCAAATGATCTCTGAGGACCCATTGACATTAAGTAGTGCCAGCTCAGGTGACAGAAGGGGACTTTGTTAAGCCGTAGAGAAGAGCCTAGGATACGGATGAGCAAGGGACTGCAGAGGGGACCATACAATCCATTTCCTGACCCTTCTCATCTGAAGCATAGCCAATGCCAGCACCAGCTATGGAGGAGACCATTTAGCCTCACAGACAGGACTAAGAAGAGGCCTGGCAGGGAGAAGAGCTCTGGTATCCAGGGGTGTGGCACCATGACCTCCTACTTTGCATCTGAGTTCAGCTACCAGGGATACTTTGGTGAGCCTTGGTTGAAAGCCCACATGGACCCAGATCTGGCTGGGTGAGGGGACATAGGTTACTGAGGTGACTATGGAGACAGGGCTACATATAGGGGTAGAGAAAAAAAGATCCCTGAAAATAAGAGGGTCCAAGTCAATGTAGGACCCCAAGTGGGTCCCTGAGGATGTAAAAGATGGGTGGAGGCTGGAAGCCGAGCAGGCAGAACACGGTGGCTCCCACTTAGGTGTCTGGTTGTCAAATCAGTACCATTTTAGGGAGAATCAGTCCTTAGATTGATTTCTTTTGTCCTATGATCCCATCTCTTGACTCTACAAGACCAGAGCCTAGAATGGCTGGTCTCCTTATAACAGCAGCGATGATGGAAGAGTCTGTGGGGATGGTCAACCCCACCACCATCCCATCCTTACTGAGACCGTGTCGGTCAGATGGTGGAGAAAGGATGAGCTAGGACAGCGGTTCTCAACCTATGGGTTGCGACCCTTGGGGGGGGGGGCGTGTCACACATCAGATATCCTGCATGTCAAATATTCACCTTATGACTTATAACAGTCACAACATTACAGTTATGAAGTACTGACAAAAGGATTTTACAGTCGGGGGTCACCACAACACAGGGAGCTGTATTAAAGAGGTGCAGCATTAGGAAGGTTGCAGACCACTGCCCTAGAAGCAGGCAGATACATCTTGTTTAACTACATTCCTATGCAGTCTGTTGTCCGTTTTACCCATGAGGGAACAGGGGATCACAGGTTACTAGGCTTGCTTCAAGGCACCAAAGAAACAAATGGCAGCCCTGGATATTTAGCCTGGAGTCTGGCTTCAAAAACACCTGCCCTTCCTGATTCCCCCAGCTGCTTTGCTTCGTGTTAGGCAGCTGGGAGTTGTCGGTTTCTGTCTTAGCAACCATCCATTGCTATAGTCTTGGAGGCACCGAGATGAGAAGAGGATGCTTCACAGATGGCAGTGACTCATGTGTGATGGAGATTTGGCTCTTTCCATGGGATGCTCTGAGAGTCGCCCCAGGGAGGAACCTCATTGGCCCTTAGGAATAAAGACTCTTCTGGAAGTGACTTGTTCCCATCAAGAATCCCAAACTTGGGTAGGGGCGTTAGCTCAATGGTAGAGAACTTGTCTGCCCTGTGTAATAAGGCCCTAGTTTTAATCCTTAGCACTAAAACTAGAACAAGCAAACAAGCAAGCAAGCAAACACCAATGGCCACCCAAAGCCTATTATAGACAACCAGCCCAGCAAGCTATCTCAACCCAGGTTTCCTTAAAACATACTCACCAGGCCTGGCCCTGCTCACCCCAAGAAGAGCTGTTTCTGGGAAAGTTTGTGAGCTACCAGAGATCAACCATGTGGCAGAGCCCCCTGCTCTCTCCCTCTGTCCTACCTCCTCCTGACATACCTGTCCCTCATGTGCCCTTCCTTTGTCCTTCTGCCTTTCATGACTGTGACAGTTCTCCTCCCTAGTCCTCCCCATAGACCGGTCTTCCTAGCAGTGGCTGTCCCCACTGACCACCCATGGCTTCCATCCCAG
Seq C2 exon
GTCCTGTCCCTGGGTGCAGATGTGCTGCCAGAGTACAAGCTGCAGGCACCGCGCATTCACCGAGGTACCATTCTGCACTACAGCCCCTTCAAGGCTGTATGGGACTGGCTCATCTTGCTCTTAGTCATCTATACAGCGGTCTTCACGCCCTACTCTGCTGCCTTTCTGCTTAGCGACCAGGACGACTCACAGCGTGGTACCTGCGGCTATACCTGCAGCCCGCTCACCGTGGTGGACCTCATCGTGGATATCATGTTTGTGGTGGATATTGTCATCAACTTCCGAACCACCTACGTCAACACTAATGACGAGGTGGTCAGCCACCCCCGACGAATCGCCGTCCACTATTTCAAGGGCTGGTTCCTCATTGACATGGTGGCTGCCATCCCTTTTGACTTGCTTATCTTCCGCACTGGCTCAGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001901-Kcnh6:NM_001037712:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.237 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0052026=Ion_trans=PU(31.0=45.8)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000001965





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000102516, ENSMUSP00000116425
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr17:63530543-63533885 
LOW PSI
HsaINT0084366
(KCNH6)
Human
(hg19)
chr17:61607904-61611246 
LOW PSI
HsaINT0084366
(KCNH6)
Rat
(rn6)
chr10:94213755-94216805 
LOW PSI
RnoINT0077782
(Kcnh6)
Cow
(bosTau6)
chr19:48497643-48500823 
BtaINT0079609
(KCNH6)
Chicken
(galGal4)
chr27:2684434-2688378 
LOW PSI
GgaINT0142993
([1])
Chicken
(galGal3)
chr27:2597890-2601834 
LOW PSI
GgaINT0142993
(KCNH6)
Zebrafish
(danRer10)
chr12:9283134-9286796 
LOW PSI
DreINT0084868
(kcnh6b)
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"