Special

MmuINT0085831 @ mm9

Intron Retention

Gene
ENSMUSG00000058740 | Kcnt1
Description
potassium channel, subfamily T, member 1 [Source:MGI Symbol;Acc:MGI:1924627]
Coordinates
chr2:25768175-25771386:+
Coord C1 exon
chr2:25768175-25768237
Coord A exon
chr2:25768238-25771298
Coord C2 exon
chr2:25771299-25771386
Length
3061 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATT
5' ss Score
8.83
3' ss Seq
TTAGGCTATGTCCTTTTCAGATG
3' ss Score
8.77
Exon sequences
Seq C1 exon
AGGACGTAGCAAATTTAACAGCCAGTGATGTGATGAATCGGGTAAACCTGGGATATTTGCAAG
Seq A exon
GTAATTCTGCTCCAGTGAATACTGGCCACCACACAGGGGATATGTCAACCCTTTGCCACCTTGGCTGGGCCAGGCAGAGACCAGAAAAGAGGGCTTTGTGTGTCCACAGTGGGTTCTCAGACCTTCTGCCTCCCTCCTTGGTTTGGGCCTCCTAGCTGAGGGCCATGGGAGCCCAGATGATGGAACCCACCCTGGTCCCAAAATACTTGACCCAGTTCTGTTAGGATGTGCCATGCCACCTAGCTTTGGACTGACTAGGCAGCAGGCTATCCCAACAACAGCTGGTCTCTCTGGCTAGTCCCAAGAGATGCCCAAATTCCCTGTGTGTCTCAGTAGGCAGGCATGAGGATGGAACTTAGCGTTGGCTTTCTGTGCTAAAGCATAGAAAGACCTGGATTACTCAATCCAGGTAGACGTGGGGGCTCCAAGAGAAGTCTCTTTCTGCTTGAGACAGAGATCTACTTACTTCTCATCTGTGTGCTTCACCTCCTCTAAGGAGCTCTCCCTCCCTGAGGCCCAGAGCAGAGGCTAAGCCACTGCCTTTCAGTGTCTCCCCTCAAAATAGGTTGTCAAGGAGCTTTTGGGTTATCTGAGCTCAGTTAAGCTGGGTCCTTATTTGCAAGGATGGCTGTGGGAAGCCACAGAAGTGAAGTGTTGGCATCTCTGGGCTTGTGGTTTTTCTCATCCTGCCACCCATAACAGCAATCACGGAAGCTGGGCCCTCTGCTGGGCACTTGGGGTTTTGATCTAGGGCTGGTGACTTCCATGAACCAAGCGTATCCTGCACCCAGTTACATCTGCTTCCTGTGTGGCTGCTAGGCAAAGGTGGGCAGGCAAGGGCTTGGGCAGCTCCTACAGGGTCACAAGATGCTCTTGGGTGTGCAGTGAGTGTCACCTATGTGCTCACTGGAGAAAATGTGCTGGGACTCAGCAACAGGAACTCACAGTACTCTACGGGCATCATGGAGTGGCATCAGGATGTCTGGCCAGAATGTCACACTGTGCTCAGAAAAGGGCAACACCAGGCAGGGGTTGGGCCCAGAGGCATAGCCACTGGAGTTACTCTGGCTCTGGGATGAGCAAGCTGAGAATCCAGTTATTACCCTCTAGCTACATGGGAAATGGATGTAGAGGGCCAGGGCCTGAATCTCGGGGTTACTGGGCTGGGGGAAGGGGAAGGAGGAGAGGGGACACAGCTGTTGCAGAGGCATGATCTGTTGGGAGTTTCCATTCTAGAAGTGCATTCAAGCCAGGTCTTGTCCCCACCTACCCCTACACCTGCTGTCCACCTTTCCCAAGCATGGGGGCTGCCGAGGCCATCTTAGCTTGCCTTCCCCATCCCAGCAGTTGGGAGTCAGTGCCACAAGACTGACCACAGCCCCTCCTTGCACTACAGCTGGAATTTGGCATGGCCCCCTCAACTCAACACTGAGCCAGGCCTAGTCCCATCCTGGGCTTTGCTAGTCTCAGACATTTCAAGATCTGACCTCGGTTGGAGGAGAATCATGACCCAGGGCCTAGCCCTGACAGGGGAAGATTCATCAACAGCTTCTCACAGCCAGGCTTCTAGCCCCACCTTTAGGATGACTGTATGGTGGTCATGACAGAAATGAATCAGTACTGTGGTCTGAAATGTTGTGCTCACACCCGAATACTCTTGCTTCTGCACAAACCCTGCTGTCCCTGCATTACCCACGCCACTGCATGAGGGCCTTGGTCCCAGAATCACACCTCTCCCATTTGGCTCCCAGCATGAGTCATACCATGGGTATCTTGACTGTAGGATTTGAGGGGGGAGGAGCAAAAACTGATGCTCATGCGACAGAACAGCCTTCCTATATGGAGGGCAAGCCACCAGGCCTTCCTACCCTGCAGAAGTAGATGGAGGTGTTGACTCCATTTCAACTACCCCAGGTACAGACTGTTTGAGGTGCCCCCCCCCATTTCTCAGAAGCATTTTGTGCCACATTCCTTCATCCTGGAGCTACAGTTCTGAGAGCGAGGCATGCCCCTCCCTGGCTCAGTTGGCTACCTGGCAGATTCTTTAGTTTCACAGAAGGGTCAGTCTCTTTCTTAGGGTTATGTCCAGCATGACCAAAGGATAGAGAGAAATGGAAGGAGCCAGGTAGAAGATGCCCTGTCTCAGGTCACCTTCATTTTGTATGCTCGTTGAGTCCAGAGATACTTCTAAATATGAAGTAGGTAAATTGAGGTCAGCAAGCTAAGGGCCATTGCCAGGACTGTATGAGGCCATGGTGACCTGCTGGCCAAGCACAGGCACCAATGAGATAACAGGCTGCTTCTCTGGACGGGCCACGTTCCCATGAGTCAGTCCATGGTCACCCTGGGGCTAGGAGCTTGTGGCAGCAGAGCCACAAGCAGGAGGGAATGACCCTGTTCTCTGATCAATGAGTCCGAAGTATAGGGAGTAGAGGTGGCCTTCCCAGCCCCCAGGAATGGGGGTCCTGCAGAGCACTTCAACTGAGGTTGCAGCTTATGTACGTATGTAGGTGTGAGGTAGATGGAGTGTGTATGGGGGGGGGGTGTGCATGTGGGTATGTGTCATGTGCAGGTGACCAGTAGTGTTTATGGGTACACAAATGTATATGTACAGGTGCAAGTATATAGGATATGCACAGGTCCTTGCAGGTGTGTTTAAGTGTGCACAGTTATATATTCAGGTGAAGGCATGCATGGATATGCACAGGTGTACTCAGGTGTGGTGCAGGTATGTGTACATCTGAGCATATGCACCTGCCCATACAGATCTATAAGAAGCAGGCATGTACAGGTGTGCTCGGTAACTCTGTCCTGGCCCCACACACTGGTGAGACATCATCTAAGGTTGGCTCGCAGCTGAGCAACCTGCGCAGGCAAGTGGGAGCCAGTGCTCTGCTCTTCCTATGGCTGAGCCCTGCCAAGTGCAGGCAGGAGCTGTGGACAGGTGTCAGAATCCATCTGTGGCCAGAAAGGAGGGACAACTCGCTCCCCTGGCTCCTTGGGGCCCCGCAGAGCCGTACTGGGTGGGGCTGTGGTGACACTTAGGCTATGTCCTTTTCAG
Seq C2 exon
ATGAGATGAACGATCATCACCAGAACACCCTTTCCTATGTACTCATCAACCCCCCGCCAGACACAAGACTGGAACCCAACGACATTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058740-Kcnt1:NM_001145403:30
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.455 A=NA C2=0.633
 
                        

				
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, ENSMUSP00000046284, ENSMUSP00000109809, ENSMUSP00000132212
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:135786522-135788099 
ALTERNATIVE
HsaINT0084716
(KCNT1)
Human
(hg19)
chr9:138678368-138683642 
ALTERNATIVE
HsaINT0084716
(KCNT1)
Rat
(rn6)
chr3:3358807-3360052 
LOW PSI
RnoINT0078060
(Kcnt1)
Cow
(bosTau6)
chr11:103434750-103437761 
LOW PSI
BtaINT0079869
(KCNT1)
Chicken
(galGal4)
chr17:8212984-8214940 
ALTERNATIVE
GgaINT0123780
(Segment)
Chicken
(galGal3)
chr17:8907991-8909947 
ALTERNATIVE
GgaINT0123780
(KCNT1)
Zebrafish
(danRer10)
chr5:64908504-64915523 
ALTERNATIVE
DreINT0013232
(KCNT1 (2 of 2))
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"