Special

MmuINT0085455 @ mm9

Intron Retention

Gene
ENSMUSG00000058248 | Kcnh1
Description
potassium voltage-gated channel, subfamily H (eag-related), member 1 [Source:MGI Symbol;Acc:MGI:1341721]
Coordinates
chr1:194062607-194065919:+
Coord C1 exon
chr1:194062607-194062735
Coord A exon
chr1:194062736-194065800
Coord C2 exon
chr1:194065801-194065919
Length
3065 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCGT
5' ss Score
9.49
3' ss Seq
GTGTTTTCTGCCTGCTTCAGGTT
3' ss Score
10.49
Exon sequences
Seq C1 exon
GGACACCTGTGTGGTTTTTTGTGAAGATCGCTCCGATCAGGAACGAACAGGATAAAGTGGTCCTGTTCCTTTGCACTTTCAGCGACATAACTGCATTCAAGCAGCCCATCGAGGACGACTCCTGCAAAG
Seq A exon
GTGCGTAACCCTGCTCGGTGCAAGCACACTCTTGCTCTTGCTACAGACAATTCGAGGTTGCCAAGGCAATCTTGTGCAGAGATCAGGACTTCAATCTTAGTTTGCATTGGGTGCTGTGTCATTCTGCAGTGTGCTTGGGCAAGAGCGGCAGAAAACGTTTGGTAAAGCATTTAAAAACCCACCATTCCATAGTTACACTTGGATAGAGGAAGGCAGCCCAGCACGTCTGACCTCATGGGGCTTTTCAGGTTTCCTTCCCTTTCCCTCCATCCCTTCCCCTACTGGAGACTGAACCTACAGCCCTGTGCACACCAGGCAATCACCTCCACCTGGCTATGAAGCTCTTGATGGTTTTCACAGCTGCCCACAAGGGGCAGGCAGGCTGTGCTTACCCAACTACTTTCTTGTGGACATCTTTGGGTCTGACTTGTGGATGGTTGCAGTCTCTTTAGATTAAAAACTAGAAATGAGGGAGTGATGAACCTGGAAGATGGGGCAGGGAGGTGGCAGGACGTTAGTAAATGACTGTGTGTCTGCTATGCTCTTGAAGCCAAAAAGTGGATTGAATTTACTCATCTGAGCTGTCAGAGGATTAGGGCAAAGTTGGATGCACTCATACACCTAGTATCATGCTCTGAACCGCACATATGTGTCTACATGTGACTTACATGTGCTTGGTCGCATCATATTTGTGGTTTGTTGTCTGTGGCTAGTTAATTGATAGGCAGACATTACTGAGGCCATCGGCCAGAGTAACATGTCTTAGGGGTCATTTGATCAGCTGAATGGCCTTAGGCTTTATCTAGATCGTGGGTGTGTATTGTTTGGAAAGCACCGAAGGCTTCGGAAAGGAGCCCTGCAGGATGGCTGGGTGAGCTGGGCTCCTGCACTGGCTCACTGAGGTAGCAGAGAGCCAGTGTCAACCACTCTTTCACTCCCTGTCCTGCAGCTGGCATTCACTCAGTCAAGAACCCAGCAGTGCTTCATGTTGTCCAGCTACCTGGCTCTGTGCTTGGCTTTCTCCTCCAGCTCTCTGCTGTTGAGGGTTCCTGGGATGAAGCCGAGAAATGCCAGTGGAGTCCAGGGGAGAGACAGGCTGGGACTCGTTACCCTGGATGTGACAAAGACTGTTAAAGAAGCATCATAGGGGAAATAAGCATGATTTGGTCATGTGAAAGTGTTTTCTGCGGAGATGCAGCAGTGCGTGTCGCTATTATTGTTATAGTAGGAAAGGCATACTCTTCTGAGAGTGCTTCTTATCTGGCTCCACCAAAGTGATGAGTCGGTGTGACGGTGGGAGGCTGTCTTGGGTTAATTTTCCACAAGTCATGTGCTCCACTTATTTAGCCCAACCTGCCCCCATAGTGCATCTTGTTGCTGATGAGAATCTCAGTGCACACAGCAGTGCATTCCCTGCTCCCCTCCAACTATTTCATTAGTCAAGGTAACTTCTTGTCGTGTGTCAATTCCTTTTTGTCAATGAAATAATACAAGTACCATGTAGCCTTATTTGTAAACAATTTAGAACAAGTACATACATAACACATATTCACATATAAACACCTGTACCTGTGTAGAAACTCACTTGCATACATATGCACACATACATGCATATATGTGCTTATACACATATGTATAGATACACAACCATAAACACAGAGGCATATACATGCACACACATGTCAACACATGTACATGCTCATACACATTAGTTTTCAATGTGAGAATCCTGGTAGGGAACCCAGCTTCATGTTACCTGAAAGTCCACTGCTGTGTTCTGATTCCCACGCTTCCTCTGTCTCCATACCCCTGATCTGCTGTGGTGTTGTGGTCTGCTCAGGACAAAGGTCAGATTTTATGTTAGCTTGTTTATGATGGAAAAGCCTGGGAAATGGTGAGATTACCTAACTGTTAGTCTGCAAACTTCAGTTCTGGTTAAAAGATCTGATCCAGATGGGAAAGATGCTACTGCGTGACTGGATTGCTCTGCGTTGGGTTTGCTTTCTGGATATGCTCTTGGTTCTCTCTCCCTGACCCTGCTGTGTTTTTGGTTCAGTACCACAGTTAGCACCAAGTCTTCAGTCTGCTTTCCCAGGCTTGTTTAGAATTCACTGTGAGCTTGACTGGAAGCAAGGAGAAGAGAACATGCAGAAAACTCCCCAATAGCCTCAAGGGACATTCCCTACTGTCTGATTAGTTTTTTAAGTCACATGTGTTCAAATTGTATTTTAAATTATATGGCCTTGGTCGTGTACTTCACAATTTGAGTGCCTAGGTGGTATGGTGTACGTCATGGGAGTGGTTCAGGAAGCCTGCTTGTGCCTAACATTTTTCTCTGAACAATTAACTCACAAATGGGAAACAACCAGATAATAGAGTTGACAATTTTGCATGGAGTCCTGGGCACTGCTGTCGGGCTCTGGGATGAGTCACTAGACTGCCTTCACTCATAGCTCTGTGTGTGACAGGGCACCTTCCTCCTTTGTTCTGCTGTCTCCCTTTGACTAATTTCCTAACTCACACATGTCACAGAGCAGGGACTGAAATTCAAGCAGGGTTTTCTGTTTGGTAACCGGTGGGTGGGTTATACCTGGGCTCAGAGAGAAATACCTCCTGTTCCAACTGTTGGTCTTTCTCTCTGCTTCTTTCATGGAAAGCAGGTGCAGAGCCTTTACCTTCCTCTCTGCTGAGCTCAAGGATTGATCAGGTGTGAAGTGTGGGGCTTTGGCTGTCACCTCTACATTGCTCACAAAGACGAGTCACCCTCTTGCTGTCTTGTAACTTGTAACAAAGGTGTACACTCACCTGTGTGTTGGAACGTTACATTTGAACCCCACCGGAGATGGTGTAGCTTAAGTGTGTTGGAAAAGCAAGTTGCTGCCCAAACCTCGATATTTCAAGGTTCATATCTGAGCAACTGGTCTTGCTTGCCTGCAGGCATGAGAGATGGGCTCATTGGAGCTCCAGAGGACCCTGGACATTGTCCTGTGGTGTTGGCGGATGAAAATGCCTGTGTTCTCTTAGTGTGTGGCTAACCTTGTCTTCGTGTTTTCTGCCTGCTTCAG
Seq C2 exon
GTTGGGGGAAGTTTGCCCGACTGACCAGAGCTCTGACAAGCAGCAGGGGAGTCCTGCAGCAGCTGGCCCCCAGTGTACAGAAGGGTGAGAATGTTCACAAGCACTCGCGCCTGGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058248-Kcnh1:NM_010600:4
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:
PF134261=PAS_9=PD(29.2=70.5)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000077563





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000106468
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:211082899-211090561 
HsaINT0084298
Human
(hg19)
chr1:211256241-211263903 
LOW PSI
HsaINT0084298
(KCNH1)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr16:74160412-74169450 
LOW PSI
BtaINT0079546
(KCNH1)
Chicken
(galGal4)
chr3:21690276-21698732 
ALTERNATIVE
GgaINT0086962
(KCNH1)
Chicken
(galGal3)
chr3:23501478-23509934 
LOW PSI
GgaINT0086962
(KCNH1)
Zebrafish
(danRer10)
chr22:37956455-37958751 
ALTERNATIVE
DreINT0084773
(kcnh1b)
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"