GgaINT0124101 @ galGal3
Intron Retention
Gene
ENSGALG00000005045 | CDK9_CHICK
Description
NA
Coordinates
chr17:5526438-5526831:-
Coord C1 exon
chr17:5526660-5526831
Coord A exon
chr17:5526587-5526659
Coord C2 exon
chr17:5526438-5526586
Length
73 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGA
5' ss Score
7
3' ss Seq
TACAGAGCACCTCTGTTTAGGGG
3' ss Score
1.54
Exon sequences
Seq C1 exon
ATCTTGCATCGAGATATGAAAGCTGCAAACGTTCTGATCACGCGGGATGGAGTCCTGAAGCTTGCAGACTTTGGGCTGGCTCGAGCTTTCAGCCTGGCTAAGAACAGCCAGCCGAACCGCTACACCAACCGGGTCGTGACTCTGTGGTATCGGCCGCCGGAGCTGCTGCTAG
Seq A exon
GTAGGAGGTGATGGGTACCGCTGGCTTCTCCTCCCTTCACGTCCCAGGTGACTTACAGAGCACCTCTGTTTAG
Seq C2 exon
GGGAGCGGGACTACGGGCCCCCCATTGACCTCTGGGGTGGAGGCTGCATCATGGCAGAGATGTGGACCCGCAGCCCCATCATGCAGGGGAACACGGAGCAGCACCAGCTCACCCTCATTAGCCAGCTCTGCGGATCCATCACACCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005045:ENSGALT00000008092:5
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:
PF0006920=Pkinase=FE(19.2=100)
A:
NA
C2:
PF0006920=Pkinase=FE(16.5=100)
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:
GAAGCTTGCAGACTTTGGGCT
R:
CCACATCTCTGCCATGATGCA
Band lengths:
181-254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]