GgaINT0048443 @ galGal3
Intron Retention
Gene
ENSGALG00000012444 | AVR2A_CHICK
Description
NA
Coordinates
chr7:36178718-36180932:+
Coord C1 exon
chr7:36178718-36178856
Coord A exon
chr7:36178857-36180801
Coord C2 exon
chr7:36180802-36180932
Length
1945 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
TTGCTGTTGTTTATCTCCAGGCC
3' ss Score
10.22
Exon sequences
Seq C1 exon
GTTGGCACACGAAGGTACATGGCTCCTGAGGTACTAGAAGGTGCTATAAACTTCCAAAGGGATGCGTTTTTGAGAATAGACATGTATGCCATGGGCTTGGTCCTCTGGGAGCTGGCATCGCGCTGCACTGCCTCAGATG
Seq A exon
GTGAGCAAAATCTGCTGAAATATGTTGAAATGCTTTATTTAAATGGGTGACTGTTTTAAACAAGAGATTGGAAGGTAGGTTATGTGCGTGCAGTAACATGCGTTAAGGATGGCAGTCTTGTGAGCAAAGGAATTAAACACCAGCACCGTGCAGTCACTTCATAATTGAATCTCTTCTGTGTATGATGTCCCACCATGTATTTTTTTTTCCTCCTGGAGATGGCAAGGAGAGGGAATTGCTGCTGAATTCCTAACCTGTTTGATTTCCTGAGGTCAGCCTGACAGCGTCAGTGCCAACCAGTTTGTCTCTCAGCACTGCTTCTGTTCTGACATGAAGAATTTTCACTGGTCAACGTGTATTCTATTACAAAGGGCACGGTTGCAGCTAGTGATGTTCTGGCTGCTCCTCAGCATGCATACAAACCTTGGCCCTTCCTGGATCCTGGTGAAATGAACCAGTGGAGTGAGAAATAAAGAAGATTCTGCTGCTGATTTAACTGTAGGTGTGAGTGAGGCACTGCTGTGGAAGCTCAGTGCCTCCCTGCCCAGTCCTTCTCTTTGTTGGCACCGGTGTGACATGAGTTTTAATGGGAGTCGGAGGAATATGCCAAGGAATTGCTGATAGCTCAGAGACTGAAAGCACGGCTGTGTCAGCGACGTGCAGCACTCTGAGCTCTTAGCTGGGAGTCCATCACAGCTGTGTATTTTTCCATGAAGCAAACTGTTTGATCCAGTTTTTAAGCTATCAAGAAAACATTTCCAGTACTATATTTCAAATATGAACAGTTCTCTTAAATTTAAGCAGAGAAGTTTTTATGGTGCCCAGCATAAGTCAGGGTTAATGCAGGACAACAAAAGACAAGGCTCAAAACATTCAGGGAAAGTTCACTTTGCAGTAAAGTCTTTAATGAAACTAAGTAAATGTGAGAGCTGTGCTTGGGCTTCTGATACCATTTGTCAGAGAGTTCTCCTGGACCCGTGCAGCTGGAAAACATCCACTGAAAAGCCAAGGTGTGGTGGAGATCTGAGATCAGCGCGAGGTCACTCAGAGCTTTTCTGCTTCAAATACTCCTCGCAGAGTGGCAGCCACGAGGGAGGCTTTACCCTTTTAAAAATGTTAAGCTGTTTACCAACGGGATCGATGCGCTCTCGGAGGCAGACCCACATTCTGTATTGATTTCTCCTGCCTCTTTGTACTGTAAAACATCCTTACCTAAATCTTACTAGAAGTGTGTTGTAGATCTCTCTGGCAGGTGTGGTCATTCCAGAAAGCAAAGGAGGTGTGAAAGGAAAGCAGCCTTCCTGAGTCACAGCTGTGTGCAGCTCTGCACTCAATGCTGCTCTTTCTGTCTCTGAATTGCTTTGTTTTCAGCAGGTACCTGGAGTGCTCGCTGAGCCTCACTGGGCTCTGTGCTGTGCTCTTCTGCCCATCTTCCCCTTCCTCCTTTCCCTGTGTACCTTTTTTTTTTTGACTTTTGATCTCAGAGTACAAAATGCATACGACAACATGTAATCTATAGCTACATAAGCTGCTGTTCAGCTGAAAGTGCTTACCCCTCCTGCTCTTAGCATCCACACCAGGGCACCGGGTGCCTGTTGGGTGAGCAGACTCCAGAGGGCCAACAAATATGGAAGAAGGACGAGCACCTACCTGAGCAAAGGGTGTTAGAAGAGCTGTGTGCAGGAGCCTCCCTCCCTTGTGCTGTGTGCAGGCAGCCGGGCTGGGAGCTGCGTGTGGCTGCCATGGCTGGGAGAGCAAAGGCTCTGAGCTGCTCAGTGAGGGGCTGAGCTGCTGCTCACCTGGCACAGCGTGAGCTTTAGCAGCACCAGAAGCAAAACTACAATATAAGGCTCTGATTATGGGCTACGTTTCTAACACACAAATCTTTTCCCCTCTAAGCAGAACCTGTGTTTTAACTGTTTTTGTTGCTGTTGTTTATCTCCAG
Seq C2 exon
GCCCAGTAGATGAGTACATGTTGCCATTTGAAGAAGAAATTGGCCAGCATCCTTCCCTTGAAGACATGCAGGAAGTTGTGGTTCATAAAAAGAAGAGACCTGTTTTAAGAGAGTGTTGGCAAAAGCATTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012444:ENSGALT00000020344:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006920=Pkinase=FE(15.9=100)
A:
NA
C2:
PF0006920=Pkinase=FE(14.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTGGCACACGAAGGTACATG
R:
AGAATGCTTTTGCCAACACTCT
Band lengths:
270-2215
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]