GgaINT0124097 @ galGal3
Intron Retention
Gene
ENSGALG00000005045 | CDK9_CHICK
Description
NA
Coordinates
chr17:5529688-5530102:-
Coord C1 exon
chr17:5529995-5530102
Coord A exon
chr17:5529770-5529994
Coord C2 exon
chr17:5529688-5529769
Length
225 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGC
5' ss Score
8.19
3' ss Seq
GTCTCTTCCCGTTCTTACAGGGA
3' ss Score
11.81
Exon sequences
Seq C1 exon
GAGGGCGGCGGCCGGCATGGCCAAGCAGTACGACATGGTGGAGTGCCCCTTCTGCGATGAGGTCTCCAAGTACGAGAAGCTCGCCAAAATCGGGCAGGGCACCTTCGG
Seq A exon
GTGAGCGCTCCGGCCCTCGGGCCTGCTCCCGGCGGGGCCTGGCTCCTTCCGGGCCTATTCCCTGCGGCTCCTCGGCGTCCTGGGGCCCAGGCCGCGGCCTGACCCGGGGCCTTTGTGCTGGGGGTGGCCGGGGTGGGGGCCGCGGCCTCGCCCGCCTCCTCACGGGGCCGCGGGGCCGTCCGCGCGGTCCCTTCCCTGCTCACGGGTCTCTTCCCGTTCTTACAG
Seq C2 exon
GGAAGTGTTCAAAGCCAAGCACCGGCAGACGGGCAAAAAGGTCGCGCTGAAGAAGGTGTTGATGGAAAATGAGAAGGAGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005045:ENSGALT00000008092:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=PU(16.7=38.7)
A:
NA
C2:
PF0006920=Pkinase=FE(37.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGCCAAGCAGTACGACATG
R:
CCCCTCCTTCTCATTTTCCATCA
Band lengths:
174-399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]