Special

MmuINT0085515 @ mm9

Intron Retention

Gene
ENSMUSG00000001901 | Kcnh6
Description
potassium voltage-gated channel, subfamily H (eag-related), member 6 [Source:MGI Symbol;Acc:MGI:2684139]
Coordinates
chr11:105887108-105888186:+
Coord C1 exon
chr11:105887108-105887192
Coord A exon
chr11:105887193-105888029
Coord C2 exon
chr11:105888030-105888186
Length
837 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGTCCCCTTCCTTCCTGAAGGTG
3' ss Score
10.23
Exon sequences
Seq C1 exon
GCAGATGGGGGTCTCCACTCAACACCCCGACAGGCCCCAGGCAACCAAGACCCCCAAGGCTTCTTCCTCAATGACAGCCAATCAG
Seq A exon
GTGAGTCCAGCCAGCCCCTACCCAGGAGTCTTGTCCAGCCTTTATCCCCTTCTAATGTCCCCACTATTCTGAGTCTCCTTGAAGAGGGTGTGTCAGCCACTAGGCGATAAGGAAAAATTCTTCCTTGGGCAAAGAGATAGTAGCTTTTATCTTTTTCTCCAACCCTGCTGGCCTGTATCCTATGAGTCAGAGAGGGAGAGCTCATTAGCTGCCGGGTGCTTCTTTCAGGGATGGGTACTAGCCAAGTGCCTGAGGTCCTGTATCAAGGTACTAGTTGCTGGGTGCTTCTTTTGAGGGTGGGTACTAGCCAAGTGCCTGAGGTCCTGTATCAAGGTACTAGTTGCTGTGTGCTTCTTTGAGGGTGGGTACTAGCCAAGTGCCTGAGGTCCTGTATCAAGGTACTAGTTGCTGGGTGCTTCTTTTGAGGGTGGGTACTAGCCAAGTGCCTGAGTTTCTGTATCAAGGTACTAGTTGCTGGGTGGTTCTTTTAAGGGTGGGTACTAGCCAAGTGCCTGAGGTCCTGTATCAAGGTACCAGGAGATTCCTGTCCCTCTCCAGACTTTGCTCTATGAGCAATAAGACCAGAGCTAGAAGTCCTCACCCCTATCACTCCATTGAAGTTGAAGCTCCCAACTCCCCTCCCACGGATATTCCAGTTGGGGTCTGAAAGCCAGACCTCCGTAGGAACAGGACCTTGTCCTCAGAGCACCCAGGCAAGGAGAGCCACTCCTTATACTGTGTTCCCGAGACAAGAAGAGGGAGCAACACGGGCTTTGGTGAGAAGGGGCAGGCCTGTGGAATCAGATGTAGCAAAGGTTGTCCCCTTCCTTCCTGAAG
Seq C2 exon
GTGCTGCCCCTTCCCTGAGCATTTCAGACACATCTGGGCTTTGGCCTGAATTGCTACAGCAAATGCCCCCAAGTCCCCCAAACCCACGAGAGAAGCTGGATTGCTGGCCTCGGGAGCTAGGCTTTAAGTTAGAACAGCTCCAAGCCCAGATGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001901-Kcnh6:NM_001037712:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.793 A=NA C2=0.409
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000001965





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000049507, ENSMUSP00000102516
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr17:63543661-63544248 
ALTERNATIVE
HsaINT0084361
(KCNH6)
Human
(hg19)
chr17:61621022-61621609 
HsaINT0084370
(KCNH6)
Rat
(rn6)
chr10:94225066-94225636 
ALTERNATIVE
RnoINT0077777
(Kcnh6)
Cow
(bosTau6)
chr19:48510067-48510579 
LOW PSI
BtaINT0079604
(KCNH6)
Chicken
(galGal4)
chr27:2693817-2694205 
GgaINT1000139
([1])
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CAGATGGGGGTCTCCACTCAA

				
R: 
GTTCATCTGGGCTTGGAGCTG

				
Band lengths: 
239-1076

			

		

	





	
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






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