GgaINT0124099 @ galGal3
Intron Retention
Gene
ENSGALG00000005045 | CDK9_CHICK
Description
NA
Coordinates
chr17:5526996-5529196:-
Coord C1 exon
chr17:5529106-5529196
Coord A exon
chr17:5527163-5529105
Coord C2 exon
chr17:5526996-5527162
Length
1943 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGCT
5' ss Score
6.77
3' ss Seq
CCTCCTTGCCTCTCCTGTAGCCT
3' ss Score
9.15
Exon sequences
Seq C1 exon
TTCCCCATCACAGCTCTGCGAGAGATTAAAATCCTCCAGCTGCTCAAGCATGAGAATGTGGTGAACCTCATAGAAATCTGTAGGACCAAAG
Seq A exon
GTAGCTGGCGGGGTCTCCTTTGTGCTGGCTGCTTGCTGAGGGGATGTCTGTTTTCAGCCTTTGTTCATGGCTGAGCAGGCTGCTGTGTTGCAGTTGGGATGGATCCTCCAGCTGAGCACGTGCTCACGTCTTTAATCTGGGGTGACCACACACTCATCTGTGGAAACTGTTTCTGAATGAATGCTACTGTGCTGCAGCTTGGCTGGAAAAAGCTGTTGTCAGTGCTGCTGGAGCGTGCCTGTGCTATCGCAGTGAACACTGTCTGTGTGCTGTCTGAGTGGCTTTAAATAAACCTGCAGCAGGAGAGAATTTGAAGCAGAGGATTTTCTGCCTGGTGGTGGTATTGCAGCGTTATGGTGCCGACGCCATTGGGAACAGGAGCTGTGCTTCTGCATGTGCTTACACAGCTCGTGGAGCTTTGTGCTGGTGACAGCTCCAGCTGGAGACATGCTCAGCCTCTCATTCTGTGCATGACAGAACCCCCCAGGCTTTGAGGGCTGGATTAGAAGTGCTGCGACTTCACAGTGAGTGATTCAGTTGCTCCGTGCTGAGCTGCTGTTCCATCTCGTTGCTGCAGGCGGTCCCTGGGGGAGGCAGCACGTCTCTGCTGTGTGACTGGTGTGCTTAATGTACCTGGCCTGGCTCAGTTTCCAGGGAAATCATTTTAAAGCATTTCCTCATTTTTGTATATCCTTCTCATGTGTGGATTTGTACTGCAAAAGCAGTTTTGAAAGTGGCAGATGATATTAAAGCCTGCCATGCTGTAGTCAGTCTTTTTGGTTAAATAAAATTGTCAGTGGCACCTTTCTGCTGCTGATGTTTTCTGCACTGAACTGGTAGAAACCTCAGGCCTAGGTCTGGGAACCTGGTGTTGCTCCATTGAATGTAGGTTACTGCCAGTTTTTGGAATCAGTAGGTACAAGGGAAAACACCAGCACCAAGTTAATTTTTAATTCTTGGTGTGATTAAATCAGTTGTGCTGACAGCGTGTTTCTGGCATGCCTGAGGTAAATATTTTTGTAGATGTGTCAAATTGTTTGGGTTTTGTTTAAATTCCAGTTTTCATCTGAATCTACTTTGACCTCAGTTTCAAGTGAAAAACAGAACCGTTCCATTTACTGTTCTCAGACTTTAAGCTTTTCTCTTTTTATGTTGGAGAGGTGTTGTAAGGACTGCACCACTGTCAGGGACTGTGTGAGCAATCTAGAAAGCATCCTCCAGGCGTGCAGGGGAGAGCTGCTGCATTCACTATGCAGGCTGAGCTTAGCCTTCATTTTCTGGTTCTTGTTGCTGATCAGCAAGTTTTGCTGTGCACAGCTGATGAAAATCAGCCTTTCATTTTGGTGTTTTGCACGTGCGCTCTAGGAACGAGATTGAAATTGATTGCTTCATTTGAGGTTTCCTGTTATTGACCATAAATTGCAATTGAAATGGGGGTTTTAAATCATACTGATCTGCATCAGTCTGTTTTCATAGATGCCATTTGAGGTTGCAGTCAACTTCACTTTCTGATGTTATTTTAGAAAGATTTTCTGTATTCCTGTGAGTCTGTCTTTGCCTCTGCCTCCTCTAATGCTGATGTAGTGATTGTGCTTGGCTAGCAGCTGTGTGTGTGTGCACCCCTGGGCTGTGGTTTCTAGGCATGAAACCCCACAGTCATTATGCACACAACACACAAATGAAGCTTTCAAAGACTTTTTTGCTCTTTCCTTGCCTTTCTCATGATATTCACTACTGCTCTGATCCTCATCCCCTGTTCTTCTGTTGCTTGTTTTGTTGTTTTAATACCTCTTTTTGAAGGATCTTGAGGCATCTGGGGTCCCTGTTTTGATGTTCCTCTGCCGAGAGGTTTCAACTAGTGAGTGAGGATGGATGGAGGTCAGGGGGAGCTCTGATGGGACTGAAAATCCCTTGCTGACTGTCCCTCCTTGCCTCTCCTGTAG
Seq C2 exon
CCTCTCCATACAACCGCTGCAAGGGAAGTATCTACCTGGTGTTTGACTTCTGTGAGCACGACCTGGCTGGCCTTCTCAGCAACACCCACGTCAAGTTCACGCTCTCAGAGATCAAGAAAGTTATGCAGATGCTATTGAATGGACTGTATTACATCCACAGGAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005045:ENSGALT00000008092:3
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(10.1=100)
A:
NA
C2:
PF0006920=Pkinase=FE(18.5=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:
CCCATCACAGCTCTGCGAGA
R:
TTGTTCCTGTGGATGTAATACAGTCC
Band lengths:
254-2197
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]