Special

MmuINT0085851 @ mm9

Intron Retention

Gene
ENSMUSG00000052726 | Kcnt2
Description
potassium channel, subfamily T, member 2 [Source:MGI Symbol;Acc:MGI:3036273]
Coordinates
chr1:142247785-142251130:+
Coord C1 exon
chr1:142247785-142247864
Coord A exon
chr1:142247865-142251030
Coord C2 exon
chr1:142251031-142251130
Length
3166 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TTTTTGTTGTTTGCTTAAAGGTC
3' ss Score
8.71
Exon sequences
Seq C1 exon
GGTCCAAGTTGAATTCTACATGAACGAAAACACATTTAAAGAGAGATTAAAACTGTTTTTCATAAAAAACCAGCGATCAA
Seq A exon
GTAAGTTGTTCCCATCACTGGCTCTTTGCATAGAAATCTACCTCAAAATTCCAGCAGCATAATATTTCATAAAAAACGTCTGCATAATAGAATAAAATAGGGATAGTATTTATTGGGAAGTAAATGTAAAACAAAACAAAACAACAAAAAGAAAACTGAAGATGCTACATCCAGTAGTTTACATGTCTCTTCAATATTTTAAGTCTCAAGATCTCACAAGAGCCAGTAGAGACTTGTGTATCCTATTTGAGTTCTGAAAAATATTAAAGAAATTAGTTTAAGGAGAGCACAAGTTTAATTTCTTTACTAAGGCAGAAGGAACAGAATGCCAAGGTCATGGATAAAGGTACATGGGGGAGGGGGTCAGAAGTTTTGTATCTCCATAAGTAGCTATTGGCAGTTATGGGTTGCTGGGCATAGGGATGTCATTTTGTTCAGTGGTGTAGTCACTGGGTGATGGTCATGCTCCAGTAAATAACCCTTGACCCCTACTCAAATTTGCAATCCCAATTAATCTCAGTGAGTTTTGAAACAAAACAGGATATGAAAATAGGAGGGGATCTCGTGAGGAAGCAGAAGTAGTAAATCAGGAGTGGGAGAGGAAATGAGAGGATAATTGGGGTGAAGATGATGGTAATACATCATATGCTTTCATAAAACAATATATTGTAATATGTCATGGTCATCTCTGCTAACAAAGAGAGTTTGAGGATAGCTTACACAACTGAGTAACTACCAAGCAACCCCGGATTATTGAGTAAAGACTTGTCTCCAAAACTTCCCTTCCCTTCCGTTGTCTCCAAAAACGACAACAACACCCACAATTTTTTTCCCATTTTTATTAGGTATTTACCTCATTTACATTTCCAATGCTATACCAAAAGTCCCCCATACCCATCCACCCCCACTCCCCTACCCACCCACTCCCCCTTTTTGGCCCTGGCGTTCCCCTGTACTGGGGCATATAAAGTTTGCGTGTCCAATGGGCCTTTCTTTCCAGTGATGGCCGACTAGGCCATCTTTTGATACATATGCAGCTAGAGTCAAGAGCTCCGGGGTACTGGTTAGTTCATAATGTTGTTTCACCTATAGGGTTGCAGATCCCTTTAGCTCCTTGGGTACTTTCTCTAGCTCCTCCATTGGGAGCCCTGTGATCCATCCATTAGCTGACTATGAGCATCCACTTCTGTGTTTGCTAGGCCCCGGCATAGTCTCACAAGAGACAGCTACATCTGGGTCCTTTCGATAAAATGTTGCTAGTATATGCAATGAACACCCACAATTTAATTGAGTGTTTTAAATGTGAAGGTTGTTTAAACTGTCATTGTTTGTCAATGTTTCCTAATCAGTCCTGATGATAATCAATATTAAATGTAGCCTGAAGTATAAGGATGGGTGTTGCTCTTTCTAAGAAGACTTTACATTAGTAAGTATAGGGTGAGTGTCAAGTTTAACATGTTATAGCTGTCTCCTGAGAGGCTCTGCTAGAGCCTGACAAACACAGGGGTGGTAAGATTTTCTCAGTAGTAGACTAGCTTCAGCATTAAAGTTGAGAAGATCAATGCCTTCCTACCTGTATTTACAGGGAAGCCCCATCAGTAGATGTTACACAAAGGGGGCTAAATCCTCTGAGTGATGATGCTATTAATCACAGTGTTAGGACAATCATTGAATACTCACCTGACTAAAGAGGAGACCCTTCTTTATGAAACTGTAAGCTCTATGGTTAAATAAGTCCTTTCAACCTTGTGGTGTCTCGGTTCAGAATGTTTTATTTTGATGAAAGAGATGAATTTAGAGCACAAAAATCCCTCAGTACTTCAATTTGGAAACCAAGAAATGATTGCACGTTAAAAAAATTACTATTAAAGACTGCTATAAATACACTCCACAAAAAAGTAGTGTAAAAAGGTGACACTTCATTCTAGATTCCATCAAGTAATAATTATTGAAAGGCTTTTCTTGCAATTTTATGCAAAAAACACAAAGCACATACCACTGATTACAAGCATGACAGTGTTTCTGTTAATCAATGTAGTTGACCTTCGTTAGCCTTCTTTATCAGGCACCATGTTTCTCCCAACCATGACCTAAGTGCTTTGTATGGTATATGCATGTTACTCTTGATTTTCAAAAAATTTAAGATTCCAGTGGTCCTTCAACCTGTTTTCTTTTTAAATTAGGTATTTTCCTCATTTACATTTCCAATGTTATCCCTAAAGTCCCCCATACCCTCCGCCCCACTCCCCTACCCACCCACTCCCACTTTTTGGCCCTGGCGTTCCCCTGTACTGGGGCATATAAAGTTTGCATGTCCAATGGGCCTCTCTTTCCAGTGATGGCTGACTAGGCCATCTTTTGATACATATGCAGCTATAGTCAAGAGCTCCGGGGAACTGGTTAGTTCATAATGTTGTTCCACCTATAGGGTTGCAGATCCCTTTAGCTCCTTGGGTATTTTCTCTAGCTCCTCCATTGGGGGCCTTGTGAACCATCCAATAGCTGACTGTGAGCATCCACTTATTTGTTAAACCTGGTTTTTAAGAACTTCAATTTTCCCACTTCAGTACGAAACAGAATTTTTTTTCTATTCATGTACTTATCAGTACAAACTATTATGACTTCTCATGGTAAATGATGACATAATTATTATATAAACATGTAATTATAGAGATGATATATGTCATAATATAAATATAATAGGAACATTATCACAGGTAATTATTTAAACATGTTTTCTCTCTTATCAAATCAACAAAGTGCTTCAGAGTCATAAGGATGTATTACACGCAAGATGGGGGCAACTCGATTTTTGAGCTAGTTAAAGTTATTTCCCAAGTATTTATTAAAGTACGGACAGACTTGAACCAACCTTGACATGATGTAAATTTTGTGGCTTTTGACTTTTAAAACCCAGTTCTCTCACTTGTTGAATGTTCTCTGTCATTTATGGCTCATGAATTCTATGCCATTCACATTTTATTTTAGGAGAGGTTGTTATTAAAATTCAGCTACCAAGAACTTCAGTAAGTTTAGAAAATTATAACATGTGCTTTCTAAATACCTTCTAAGTGCTGAACTGAAAGATAATATTTTTGACAATTCTCTCTTTCTCTTTCATGCACCATATTGAAATGAAACCTAACTTTTTGTTGTTTGCTTAAAG
Seq C2 exon
GTCTAAGAATCCGCTTGTTCAACTTTTCCCTGAAGTTGTTAAGCTGCTTATTATATATTATCCGTGTGTTGCTTGAGAAACCGTCACAGGGAAGTGAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000052726-Kcnt2:NM_001081027:2
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:
ENSMUSP00000054623f4825A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000054623, ENSMUSP00000112887, ENSMUSP00000113333, ENSMUSP00000113535, ENSMUSP00000113535f4824A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:196489938-196492261 
LOW PSI
HsaINT0084736
(KCNT2)
Human
(hg19)
chr1:196459068-196461391 
LOW PSI
HsaINT0084736
(KCNT2)
Rat
(rn6)
chr13:57226489-57229082 
LOW PSI
RnoINT0078081
(Kcnt2)
Cow
(bosTau6)
chr16:6371140-6373237 
LOW PSI
BtaINT0079878
(KCNT2)
Chicken
(galGal4)
chr8:2708227-2712761 
ALTERNATIVE
GgaINT0038221
(KCNT2)
Chicken
(galGal3)
chr8:2734433-2739628 
LOW PSI
GgaINT0038221
(KCNT2)
Zebrafish
(danRer10)
chr5:64814670-64814900 
LOW PSI
DreINT0013214
(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"