GgaINT0142788 @ galGal3
Intron Retention
Gene
ENSGALG00000003354 | KCNH4
Description
NA
Coordinates
chr27:4501304-4503106:-
Coord C1 exon
chr27:4502892-4503106
Coord A exon
chr27:4501352-4502891
Coord C2 exon
chr27:4501304-4501351
Length
1540 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
TCTCCAAATCTCTCTCGCAGGGG
3' ss Score
9.77
Exon sequences
Seq C1 exon
GCAAAGGGGATCTGATCGGTGCCGACCTGGCCAGCAGGGACCCGGTGATCAAAACCAACGCGGACGTGAAGGCGCTGACCTACTGCGACCTGCAGTACATTGGGCTGCGGGGGCTGCGTGAGGTGCTGCAGCTCTACCCCGAGTATGCCAGCAAGTTCGCAGCGGACATCCACCAGGACCTCACCTTCAACCTGCGGGAGGGCAGCGAGATGGAG
Seq A exon
GTGGGTGCGTGTCCTCCCCCGCAGGCCCTTTCCCATCCTCGTGTCCCCAGAGCTGGGAGCAGGGCTGGGGCTCTGTGTGGCCGGGATGGGGAGTTCGTCTGCTCCGTTCTCGCGCTCCCGAGGCTCTGTGGCTCTGCCACCCCGTGCAGGTATGTCCCGGCGGCTGTTCTCAGCTCTGTGCAACCCGGGCACTTTCAAAGCCAAAGCAAGAGCGTTTGCAGCGGAGGAGGCTGAGGGGGATGCGGGGCTTGGAAGTGGGGTGGGAGGAGGTGGTGGGGGGGAGCAGACGGGACACGGCACCCCCGCGGGAAGCGGCCGAGTTGAGTCATGCTGCCGGGGGGTCCTCTGCCCACCGCCTCCCTCCTTCCTGGCTCCGGAGCAGTGGAGGGGGGGAAAAGTGTACCCCGACATCCACCGCCCCCAGGGCAGGGCGGAAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTCGGCAGTGCTGTCCCATTTAAAACAATGAAGCCCGCTGAAAAGCGGGCTGAGACTGATGACAAACGCAACATTGCCTGATGCGCTACGCTTATCAGGCCTACGCGTCCCCTGCAATATTTTGAATTTGCACGATTTTGTAGGCCGGATAAGGCGCTCGTGCCGCATCCGGCATAAACAAAGCGCACTTTGGGAGAAATCCCGGCCGACAGATTCCTTTTCTTTCTTGACTTTTTCGATTAGCGCAAGAAATAGCACATTGCCTGAGCGATGGCTTCGCGATCTTCGGCGCAAGCCGAAAAAGTCTTTGCGCCGAACATCCCGGCCCCACAGAGTGTCCCTTACTGGGGAGAGGTATGAACCAACCGAGGCGGATGCAAGCAAAGCGCGTTGTGTCCTGCAGGAGCCCCGTGCTGCCCGTGGGAAGGTGATGTTCTGACAGTGGGGTCTCGGCCGTGGCTCTGGCTGAGTTCTGGGGCCCAGCACAGCACTGAGAGCAGCACAGGACAGGCGTGGGCTGCGAACCCCGGAGCCCGGCACGGAGCTGCGGGAGTGCAGTTTGGGGCCGCGCTTTGGGCTGCCCGGGGGCACCGAGGGCTGTGGCCCGATGTGGGCACAGCTTTGCCCGCTGACGTCTCCAAATCTCTCTCGCAG
Seq C2 exon
GGGCTCGGCCGCTTCGCCCGCTCCCCGCGCCTCTCGCAGGCATCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003354:ENSGALT00000005306:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.938
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(53.4=65.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAAGGGGATCTGATCGGTGC
R:
CTGCGATGCCTGCGAGAG
Band lengths:
262-1802
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]