BtaINT0079561 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004078 | KCNH2
Description
potassium channel, voltage gated eag related subfamily H, member 2 [Source:HGNC Symbol;Acc:HGNC:6251]
Coordinates
chr4:114329041-114330611:-
Coord C1 exon
chr4:114330359-114330611
Coord A exon
chr4:114329235-114330358
Coord C2 exon
chr4:114329041-114329234
Length
1124 bp
Sequences
Splice sites
5' ss Seq
TGGGTACGG
5' ss Score
6.54
3' ss Seq
CCCCTCTCGGTGGCCTCCAGGGA
3' ss Score
7.12
Exon sequences
Seq C1 exon
GTGCTGAAGGGCTTCCCCGAGTGCCTGCAGGCTGACATCTGTCTGCACCTGAACCGCTCGCTGCTGCAGCACTGCAAGCCCTTCCGAGGGGCCACCAAGGGCTGCCTGCGGGCCCTGGCCATGAAGTTCAAGACGACGCACGCACCGCCCGGAGACACGCTGGTGCACGCCGGGGACCTGCTCACAGCCCTCTACTTCATCTCCCGGGGCTCCATCGAGATCCTGCGGGGTGACGTGGTCGTGGCCATCCTGG
Seq A exon
GTACGGCAGGGACCGGGAGCTGGGCCCGGAGTCCCTGCCGCAGCTGCAGAGGCCCAGCCCTCGAAGGACACAGCCCTGGGGGCTGTGGCCCTGTGACTGCCCACAGGGGCCTTGGGCTCCTTTAATGCACCCAAGCTCAGGCCCTCCCAGGGGGCCGGGGAGAGGAGCCCTACGTGGTGGGGGTGTGGGGCGGGTGCTGCTGAATTCTGGAGGTTTCTGAATTCGGTTCCCCTTTGGGGGTCTCCTCAAGGGCTGCGACACTCTTTGTTTCTTAAAATGGGATCAAATCCGAATGCTCCAAGGTAGGCAGTGGGGGAGGTTGTGCGACTGATTCCCACTTAGGGCCACACAGTTCCCTGTGGTACAGCCAAACCCTCACTTCCAGAGCAGAGGGAGTCTGCCCCTCTTCCCCTCGCATCCCTTCTTCTCCGCCCTACCTGTGCACGTGGACAGGTGTGCCTGGGTGCTGGGGACTTCCTGCCCTCTGCCTGTCCTCCCCTTGGCCCTGGCCACCTCAGGGCTGATGTGTCACAGTGGGGCTTAATGCTTGTGCCGCAAGCACCCCAAACACCACTGGAACCAAAGTTTTGCTAAACTGCAGTTGCTTTAACTGCATCCCGGTGTTTTCCATTCTGTGCCTGTGCTTACCTATGCTATCCTGTTTCTATCAGTAAACAAAATGCTGGTCTTGATTCACTACTGTGTTATGATCTGTAGCTTGAAAGAAACATGTTCATGGGGGTGCAGTGCTTAGCCAGGGGGTGTTTGGGAATGGGCTTTGGTGGGGGGGGCGCAATACCAGAGGAGTTAGAACCTAAGGAGGAAGCCAGGGTCTTGGGCAGAGCTGGGCATCCAGGCTGGAGCTGCTGGCTGGCCCTACAGTAGGTGGGAGGCACGGGTTCCTGGCCCTTCTCCTCCAGGGCACCGCACTGCACCTGTCCTGCCTTTGGGAGCTGGGGGCAGACGGGCTGGCTGGTGCCCCCCTGGCCCTGGGGGCTGGGGCTGAGCAACACGTGAGCAGACTGAGGGGAGGTGCCTGGCCAGGGTGACAATGCACGGAAGACAGGTGCCTGCTGCCTCCGCTGCCGCCCCCGGGGCTGAGCCCCCCTCTCGGTGGCCTCCAG
Seq C2 exon
GGAAGAACGACATCTTCGGAGAGCCTCTGAACCTGTACGCGCGCCCTGGGAAGTCCAACGGGGACGTGCGGGCCCTCACCTACTGCGACCTGCACAAGATCCACCGCGACGACCTGCTGGAGGTGCTGGACATGTACCCCGAGTTCTCTGACCACTTCTGGTCCAGCCTGGAGATCACCTTCAACCTGCGGGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004078:ENSBTAT00000005328:9
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=0.015
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
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCTGTCTGCACCTGAACCG
R:
GTACATGTCCAGCACCTCCAG
Band lengths:
355-1479
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]