Special

MmuINT0085477 @ mm9

Intron Retention

Gene
ENSMUSG00000037579 | Kcnh3
Description
potassium voltage-gated channel, subfamily H (eag-related), member 3 [Source:MGI Symbol;Acc:MGI:1341723]
Coordinates
chr15:99070026-99071424:+
Coord C1 exon
chr15:99070026-99070357
Coord A exon
chr15:99070358-99071317
Coord C2 exon
chr15:99071318-99071424
Length
960 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TTGATTTCTTGGGTCCACAGGGT
3' ss Score
8.49
Exon sequences
Seq C1 exon
GTGGATACCAGCTCCCTGAGTGGTGACAACACCCTCATGTCCACACTGGAGGAGAAGGAGACAGATGGGGAGCAGGGACACACGGTCTCACCAGCCCCAGCAGATGAGCCCTCCAGTCCCCTGCTGTCGCCCGGCTGTACCTCCTCCTCCTCAGCCGCCAAACTACTCTCCCCACGTCGAACTGCGCCTCGGCCGAGGTTGGGTGGCAGAGGGCGGCCAAGTAGGGCAGGGGTTTTGAAGCCTGAGGCTGGTCCTTCTGCTCATCCACGGTCACTTGATGGGCTGCAGCTACCCCCCATGCCATGGAATGTACCCCCAGACCTGAGCCCCAG
Seq A exon
GTGAGCCGGCCCTGGACTTCATGGCAAAGTTGTGGTGGCTAAGACAGAGGCACCAACGAGGCACACTTTCACCCTAAGTGTCCATTTGGGGTTTTTGTGTGTGTGGGTTTGTTGTTGTTTTGTTTTATTTTTTTGTTTGAGACTATGTAACCCTGGTTGATTCCCACTTTGTAATCCTGATTCTGTCTCCCGAGTGTGGGGATTACAGATGTGTGCCATGCATCATGTTTTCTCCTCCTCCTCCTCCTCCTCCTCCTTCTCTTCCTCCTCCTCCTCCTTCCCTTCCTCCTCCTCTTCTTTCTCCTCCTCCTCTTCTTCTTCCCCCTCCTCGATTTTATTTTTAATTGGTTGTAAGGCAGGGGACTGTACACATGAGTGCAGGTCCCCACAGAGGCCAGAAGAGGGCATTGGGTGTCCAGGATTGGAGTAATAGAAGGTTGTGAGCTGTTCTGTGCAAGTTCTCTGCAAGAACAAAACAGGCTCTTAACTGTTGCATGTAGTTTTATGCTCTACTCGACTTTGCTCCGGGAAGTGGCTGCACTACCAGCCCCTTCCCAGCTTCCCTTGAATCCTCGGATAAAAAACAAAGACACACATGTTTTCAATGACAACTTGCCTTCTTGGCACAACTGCAGAGGTATTTCTCCAGGCCCTATCCTTCTAGTCATCATGGTCCAAACCTGCCTGCCTTCCCTGATTGCTGCGATTCCCATTAGCTGGCTAGAGGGGGCTTACTTTCACTGTGTTACTCCAGTGAAATCTTGTGTCACTCCAATGTACTCTTCAGTAAACCACAAGCTCCTAGGGAAATGGACTGTACAAGCTTCTTAGGATGCCCAGGTCTAGCTTTGAACTTCTGCAGCAGCTGACATGTGTGAACACTGGAATGTCCCATCCTGACACCATGGTGGCTGCCTGTTGTCTGATTTGATGTCCTGCCTTGATTTCTTGGGTCCACAG
Seq C2 exon
GGTCGTAGATGGCATTGAAGATGGCTGCAGCTCTGACCAGCCCAAGTTCTCTTTCCGAGTGGGTCAGTCTGGCCCAGAATGTAGCAGCAGCCCCTCCCCAGGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000037579-Kcnh3:NM_010601:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.991 A=NA C2=0.946
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000040548





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000085588
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:49555952-49556369 
ALTERNATIVE
HsaINT0084320
(KCNH3)
Human
(hg19)
chr12:49949735-49950152 
ALTERNATIVE
HsaINT0084320
(KCNH3)
Rat
(rn6)
chr7:140907650-140908538 
LOW PSI
RnoINT0077739
(Kcnh3)
Cow
(bosTau6)
chr5:30446200-30446600 
ALTERNATIVE
BtaINT0079565
(KCNH3)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GATACCAGCTCCCTGAGTGGT

				
R: 
TGCAGCCATCTTCAATGCCAT

				
Band lengths: 
358-1318

			

		

	





	
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"