Special

MmuINT0085500 @ mm9

Intron Retention

Gene
ENSMUSG00000035355 | Kcnh4
Description
potassium voltage-gated channel, subfamily H (eag-related), member 4 [Source:MGI Symbol;Acc:MGI:2156184]
Coordinates
chr11:100613559-100616605:-
Coord C1 exon
chr11:100616448-100616605
Coord A exon
chr11:100613767-100616447
Coord C2 exon
chr11:100613559-100613766
Length
2681 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
CCCTCGCTGCCCTCCTGCAGACC
3' ss Score
10.44
Exon sequences
Seq C1 exon
ACATCATCTTGAACTTCCGCACCACCTACGTGTCCCAGTCTGGCCAGGTGATTTCGGCTCCTCGGTCCATTGGCCTCCACTATCTGGCCACCTGGTTCTTTGTAGACCTCATTGCTGCTTTGCCCTTTGATCTGCTGTATGTCTTCAACATCACTGTG
Seq A exon
GTAAGTGACACCCCCCCATCCCACCATACATCCTAGCATCTGAACTCCAACCCAGTCTCTCCCATGAGAGGAGCATCCACAAACCCAGTTACAGTCCTATCAATTCATATGCAGATAGGTGTTCCTTAGACCCTGCCATGGGCATAGCTCTGAGCCAGGCACTGGGAAGGAACCCAAAGGGTCTATGCTCTTGGAGAACTCAGCTCACAGTCTTTGAGGGAAGCTGAGAGAACCGAATGCTAACTATGGCTACCAAGGCGGCATTGGTCTGCCGCCAGCTGAGTGGTACTTTTCACATTTTTTTTATTTCACAAACAACTGATGAGCATTTAGCTGTCTGCAAACACTATATGGGGTCTGGTCAGTGGTAGAAAGAGACAAGGAACTGGCCCTCAGAGCCCCCCTCAGATTGGTGAGACAGGCAGGAATGATGGAGGAGGGACATTAGACACAGAATCGCTGAATGGGAGACGCCAGTCGCTGCATGGTCAATGCTGCACAGGTCTGGGCTGGCCTTGGAGATCTGGGCTGGAACACCAATGTATGCAAAAACATTCTGAAATCAGGCCAGCACCTGGGGGCAGAAGCATCATCCCAGCTGGGCAGGGGCTGGGGTGGTCTGGGAAGGAACTGTTCCTGGGGGAGGTGGGAATGGAGCCAGGCCTCCAAGAATGAACAGGATTTGGCTAGCAAAGGATGAGACTCCAGAGAAAGAGTGTAGTAAGGCAACCAGGGAGTCAGGGGCTGGGGAGTGTACCTGCACCCTTGTCTTCACTTGGGACTGCCTGGAAATGCCCAGAGTGGTCGATATGGAGGCCAGCCAGACAGTAGGTCTTTTCTAGTCCAAGGTGAGGCAGTGTTGCCCTGTGTCCCCAAGCCCCCTTGCCATGGTGGGGGAGGTGAGGTGGAGACCAGTTTTCCTGTGTGCTCTCCCTGCCGCACTCAGCTATAGCAGGAAACCACCTACACGAAGCCGGATTTAACTAGCCGCCAACGGGCTGTGGGCCCCTCTCCTGGTTGTGCACATGTGTGTGCATGTTCCTACACACGTGCGTGTGTGCGTGCATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAGTCTGCCCTGAGATCCTAGCCGTTCAGAGAAGACTACCTGTCCTCGGCTTGTACCCATGCCTCTATGCCCATGAGATAGTCAGCCAAGCAGGCAGCTGTGCTGCAGAGAGCCACCAGCCCCTCCTCTCAGGATGGGGAGAGGATGTCCCCTCTCCTCTCTTGCCTTCGGGAGTACGTTACAGATCGCTACTGTACTTTCACACATGTGGAATCCTTCAGCATCAGTTCTCCCGTCTCTTTTTAAATGTTGCTCTGATAGCTCTGTCAGAACTAGGTCTCCAGACTCCCGGTCTCGTATTCTTTCCCATATACGACCTGCTTGCCGGATAAGCAGGATCTCCAAATGTATGGCTTAGGGGAGACGAGGAGAAACATTGGAAGCCTGAGAACAGAAATAGAGGAGCAGACACGTTAAAGGAGCCATGCTCCCCACAGCGTTCGGGCCAAAGGACAATGAGAGAAGGATCCTTAAAGGTGCAGGCCGATGGTTGGTGTGTTTAGTTGCCTTAGAGAAGATCTGTGTTGGGGAGCCAGGGCCTCCTCCTTTCTAGCCCCGTCTGTCGTGAGGTGGTTCTGGAGCAGTGTAATGCCAGTGTGGTGAGGGCCTTCATATCAAGCCCTAGAGTCTATAGCTCTAGCTGATAAGCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAGGAGTATGGCTACTCCTTGTTTGCCATATTTATTAGAAGGCCTAATTGAAGTGTTAATAATTAGAACAAAACCAGAACATTTGGAGATATGCAGAAAGAAAGAGAAAGAGACAGACAGACAGACTTGTGTAGAATGTATAAGGTCCTGGGTTTGATCCCTGCATCCCTTTCCCCATAGCAGAACTAACAGATGTTTACAGGACCCTGGCTAGACACCAGGGCTCCATCAACCTCTAGCTCAAAGCAAGTGTCCCCCAGCCCTGCCTTCCTTCTCACCTGTAGCTGACCTACAAGCAGAAAAGCCTGTAACCTTTGGTAGTTCTCAGGCCCCTTATCTGACCCCATTCCATTCGGTACACTTTCTGACGCCTGCTTGATGGTTTCTAGGACAGCAGGGCTCTGAGCAGGGATCTTCCATAGATCATCCATTCAGTTCACCTGCTCTCTGCCAGCTCTGACGGGGGCTTGCACCTGTATCACCTACTAATGCTAGGAGGCAGCTTAGTCCCAAATGGACTTTGGTGCCCTTCATCTTGAGTCTGAGTTATAGCTCTGTTATTTCCCTGGTCTCTGACCTTGGAGCAAGTCACTTGTGTCTGTGAGCCCTATGTGGTTCATTCATCAGCAATCCAGGGTCCGGGATGATAACTGGCCCAAAGACTTGGAAGGTTGTTTTGCTTATTTTAATGAGGACTATAAATGCCTGGCATAGTGGTGGAACAATGCAAAAGAAGTCCTCAGTGGCTAAGTTAATTATTCTCTCCTGATGCATTTTAAAGTCACTTTCTCAGGACAGCAGGGATGGGGGTGGGGCTGTGTGAGAGCTCTGGGGAAGTGTGCCTGCTAACAGCCTTCCCTCGCTGCCCTCCTGCAG
Seq C2 exon
ACCTCACTGGTACATCTGCTGAAAACCGTGCGGCTCCTGCGGCTGCTGCGGCTGCTGCAGAAGTTAGAGCGGTACTCACAGTGCAGTGCAGTGGTGCTCACGCTGCTCATGTCCGTCTTTGCCCTCCTTGCTCATTGGATGGCCTGCGTCTGGTATGTCATCGGGCGCCGGGAGATGGAGGCCAATGATCCACTGCTCTGGGACATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035355-Kcnh4:NM_001081194:6
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:
PF0052026=Ion_trans=FE(24.8=100)

							
A:
NA

							
C2:
PF0052026=Ion_trans=FE(32.9=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000102984





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000102986
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:42171996-42175578 
HsaINT0084343
(KCNH4)
Human
(hg19)
chr17:40324014-40327596 
LOW PSI
HsaINT0084343
(KCNH4)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr19:42930681-42933928 
LOW PSI
BtaINT0079588
(KCNH4)
Chicken
(galGal4)
chr27:4852091-4852276 
ALTERNATIVE
GgaINT0142783
(KCNH4)
Chicken
(galGal3)
chr27:4504595-4504780 
ALTERNATIVE
GgaINT0142783
(KCNH4)
Zebrafish
(danRer10)
chr3:17430817-17432279 
DreINT0084815
(kcnh4a)
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"