DreINT0084854 @ danRer10
Intron Retention
Gene
ENSDARG00000001803 | kcnh6a
Description
potassium voltage-gated channel, subfamily H (eag-related), member 6a [Source:ZFIN;Acc:ZDB-GENE-040702-5]
Coordinates
chr3:31605793-31607485:-
Coord C1 exon
chr3:31607233-31607485
Coord A exon
chr3:31605987-31607232
Coord C2 exon
chr3:31605793-31605986
Length
1246 bp
Sequences
Splice sites
5' ss Seq
TAGGTTTGA
5' ss Score
1.31
3' ss Seq
GTTTTTATTATTGTTTGTAGGTA
3' ss Score
7.58
Exon sequences
Seq C1 exon
GTGCTGAAGGGTTTTCCAGAGTGTCTACAGGCTGACATCTGTCTTCATCTGAACCGCAGTCTGCTTCAAAACTGTAAGGCATTTCGAGGGGCAAGTAAGGGCTGTCTACGGGCTCTGGCCATGCGCTTTAGGACCACTCATGCCCCTCCCGGCGACACTCTGGTTCACAGTGGAGACGTACTGACCGCACTCTACTTCATCTCCCGTGGCTCCATAGAGATCCTCAGAGACGATGTGGTCGTGGCCATTTTAG
Seq A exon
GTTTGAGTTATTTCTAGCTCTGCCTTTCCTCTTCACCTTCATTTCTTTCAACCTGTTTAATTCCTTCCGTTAAAGGCACAACATGGACAATTATTTTTCATTAAAATATCCAAAAACCACTAGTACAGAGTTATATATTTTACTGATTATGTTCTTAGATCCTCACAAATGTTTTGAAGATTGGTTTATTTTACCTATGGGCTCAAAATGTATCCTGTGTTGCCACGCTAATGACGTCATACCCCCTCAATTTCTGTTTAATAGAAAAAAGTTTTTCTATTATGTTTTAATAGACTAACAGAGCAGCATTAAAACAGCATCTTAAAGTTGATTTAGTTTGATAAAACAACAGCTTCTTCTGCAATGATCACGAGTGGTAGAACCAGAAGAGATGGACTGTGGAATAATAAAAGCTTAGCTGCATTCCTGCTACATGGTTCTTGTCTCTCAACAGCAATCACTTCAGCATTCTTGTATCAATCTCAACAGCTTTCAGCCTTGCTTAGCTTCATACTACTATGATAATAGGTTTTGACTACTTTAGCTCATCCATGGACACGTGTTCTGCAGGATGCCTGTAGGATGTAATGAAGACGACAGCTCCTATGATTCCACTCTCAGTCACAGCATCAAAAAACTATGCCTTTATTTGTTTTAATTACACGCCCCCTACTGCCAAAAATGACATATTGTGCCTTTAATTTTAGGAACATTAAAATGTATGGTTCAATCATGATAGCTTTTAATCAATGATCATTTCTTTCAATATACACAATATCATTATCATTAAAAACCATTAATATTTCCAATTTTTCCAAGATTTTGTGGATAAAAAAATTACATAAATTATTTAGAAATAAGATATTTCGTTGTATTGTAATTTTTTACTCTCACTTTTCATTTGAACTTACATTTGTTGTATAAAAAGCTTAATTACTTAGATTTTTTCATTCATTTTTTTATCTAAACTATTAAACTTTGTTTCATAAAAGTCATAAAAACTACTAATACAGATACAGAGGTTTTATAGAATCATTAAAGTTTGGAACTTTTGAGTGTTTTCTTTGCTGGTCCATTCAATGTGCACTGTAGTGTACCTTCATATAGTAGCCACATAAAAATGTAACTCTGTAGTGCCCCTGTGTGGTGGTATTAAAACTCACAAAAAGCTTTACATGAAACCCAACTCTGATTATTTTCTGTTTCAATTTCTCTTCTAATCAAATGTTTTTATTATTGTTTGTAG
Seq C2 exon
GTAAGAATGACATTTTCGGGGAGCCCATCAGTCTATATGCCAGGCCGGGGAAGTCAAGCGCTGATGTGAGGGCTCTGACATACTGTGACCTGCATAAGATCCTGAGGGACGACCTGCTGGAGGTGCTGGACATGTACCCCGATTTCTCCGACAACTTCTGGAGCAACTTGGAGATCACGTTCAACCTTCGAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001803:ENSDART00000134201:10
Average complexity
IR
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:
PF0002724=cNMP_binding=PU(45.5=47.1)
A:
NA
C2:
PF0002724=cNMP_binding=PD(53.4=72.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTAAGGCATTTCGAGGGGCAA
R:
TGCTCCAGAAGTTGTCGGAGA
Band lengths:
345-1591
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]