Special

MmuINT0085837 @ mm9

Intron Retention

Gene
ENSMUSG00000058740 | Kcnt1
Description
potassium channel, subfamily T, member 1 [Source:MGI Symbol;Acc:MGI:1924627]
Coordinates
chr2:25747854-25748077:+
Coord C1 exon
chr2:25747854-25747928
Coord A exon
chr2:25747929-25747993
Coord C2 exon
chr2:25747994-25748077
Length
65 bp
Sequences
Splice sites
5' ss Seq
ACGGTGGGT
5' ss Score
8.27
3' ss Seq
ACCTCTCCCCAACACCACAGGTC
3' ss Score
8.2
Exon sequences
Seq C1 exon
GGCAACATCTGGGAGCAGATATTCCATGTGTCTTTCGTCTTGGAGATGATCAACACACTGCCCTTCATCATCACG
Seq A exon
GTGGGTGAGCCCCAGCCCCAAGCTCTGCTACCCAAGCCCCGCCTGACCTCTCCCCAACACCACAG
Seq C2 exon
GTCTTCTGGCCACCTCTGCGGAACCTGTTCATCCCCGTGTTTCTCAACTGCTGGCTGGCCAAGCATGCGCTGGAGAACATGATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058740-Kcnt1:NM_001145403:8
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:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000039058f5088A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000039058, ENSMUSP00000039058f5087A, ENSMUSP00000039058f5089A, ENSMUSP00000039058f5090A, ENSMUSP00000046284, ENSMUSP00000109807, ENSMUSP00000109809, ENSMUSP00000109813, ENSMUSP00000132212
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr9:135757231-135757297 
ALTERNATIVE
HsaINT0084723
(KCNT1)
Human
(hg19)
chr9:138649077-138649143 
ALTERNATIVE
HsaINT0084723
(KCNT1)
Rat
(rn6)
chr3:3340223-3340289 
ALTERNATIVE
RnoINT0078068
(Kcnt1)
Cow
(bosTau6)
chr11:103406943-103407009 
ALTERNATIVE
BtaINT0079875
(KCNT1)
Chicken
(galGal4)
chr17:8224703-8224893 
LOW PSI
GgaINT0123758
(Segment)
Chicken
(galGal3)
chr17:8920031-8920221 
LOW PSI
GgaINT0123758
(KCNT1)
Zebrafish
(danRer10)
chr5:64827436-64830035 
LOW PSI
DreINT0013236
(KCNT1 (2 of 2))
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGCAACATCTGGGAGCAGATA

				
R: 
AATCATGTTCTCCAGCGCATG

				
Band lengths: 
159-224

			

		

	





	
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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