GgaINT0010158 @ galGal3
Intron Retention
Gene
ENSGALG00000005801 | ACHA4_CHICK
Description
NA
Coordinates
chr20:8879894-8881827:-
Coord C1 exon
chr20:8881226-8881827
Coord A exon
chr20:8880046-8881225
Coord C2 exon
chr20:8879894-8880045
Length
1180 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
TCACCCTGCCCTGCCCACAGCTT
3' ss Score
9.78
Exon sequences
Seq C1 exon
AGCCTGTTTGCTGGAGAGCGCTGATTCCCTCCTCCTCCTCAGCTGGAGGTGGGCAGGTCTGACTACGCCAAATACCCAAACGCGCCCCGCTCCCTCCCTGCTTCACCAAGCGCTGCTCCTTGGAGTCGGTGGTCCACCAGCAGCAAGAAGCTGAGCGAAGGCTGCCCAAAGGGCTGGGGGAAGGGCGGCAGCAACAGCGAACAAACCGAGCAGCCAAAGCGCCCCGGAGCAGAGAGAGGAGCGAGCAGGGCAGGCAGGAAGGCTGGGTGTTCTGTGCATCCTTACCGGAGCTCCCTGCAGCCCTCCTGTATCTCTTGCGAGCGAGAACAAGTGTCCATCCGTATCCTGGGGAAGAGCATCTTCCTAGCGGGGAGAGCTGGGAAGCAAAGAATGGGAAGAATATAAATCAGTTGTGATGCCCTTCTGAAAAGAGGGAGAGAAAGGAGCCGAGGGGAATGAAGGCGGAGGATCCGGAGACTCGGAGAGGAAAAGTTGCCCCGACGGGAGACGCTGCGTCCTAAAGCCCGAGCTCTGCTCCACAATGGGATTTCTCGTGTCTAAGGGAAACCTCCTCCTCCTGCTGTGTGCCAGCATCTTCCCCG
Seq A exon
GTAAGTTTGAGAAGGCTCTTCTCCCCCTGCTCGGCTCTTTCTCTCTTTTCTCCCTCAGCGATGCTCCGAACGCCAATCCCTCTCTGCAAGGAATTTCCCCCACTCCCACACCCCCCTGCCCCGTCGCTACAGGTCCTCTAAATAAATCGCTCAGTGCTTGGCTTCTATTTTCTTCCCCTTGCACGAACAGTTGGGGAAAGGGTTAAAGCACAGCAGGGAAGGGGACATGGGGGGAGAACACACACAGAGCTCAGCCTCTTGCTGGGTTTTTCTCCCTGGGTGAAGTGTGTTAATGTGTCTCCGGGCGATGGCTGTGGTTGGGGAGAGAGCAGGCAGCGCTCTGCTAATGCTTCCCTTTGTATAATCCAGGGCAGGCTGCGGCTAAGTAGGAGCCATATTTCACGGGGGACGCGGGGAGAGCCCCCCGCTGCCTCTTCCCACTGCTCTTGCTGCAGGATGGGATGCAGCCCCCCGGCAGCCTCCAGAGAACCGAGGATTTAATATTTAATTAAACCAGCTGGCACTGCTGACAGCGCCGTCAGTGAACGTGCAGGACCGGGGCTGCTCCTTGCAGCATCCAACTTCTGAAGTCGTTGTTGAGGGAAACCCCACTCGTGTTATCCAGTCTGCATCCTCCCCCTTTCTCTCCCTTCTCTGAGGAGGGGCAGCTATGAAGCTTAGTTTGAAGAGCCGAATTTGTTCTTATTTCTTAACTGATGCATTTGATGCCAGTTTTCCCGTGTGAGTCCAACCCACGACCCCTACCCCCCTGCAGTTCTTGGAATAAAAATGCTGCTTTTCTTTCTGCCTAGCATCCCCCTTTCCTGCCTGCGGTCTCCTATGCTAGAAGCTTGCCACGAAGTGGCCACAAAAAGCTAAAGATTCAGGTGAAAATGCCCTCTGCAGTGGTTTTAAAATGGTTTTGGTGATGCCCCCAGTTTCTGCAGACCGATCCTGCTCTTCAGTACAAACCCTATAGCTTCTATACAGGTGAACTGAGCAAGAAATACACAGCAAACAGTGCCTGGGGTAGTAGGGAGGAATGTCACCACGGTGGCGTTGCCTCACCGTGTCCATGCTTGGGATCATCCCAGGGGTCCCCCCAGGAGGGCTTCTGCTCCCCCCTATGGTTCAGGGCTGCAGTGCACAGCAAAGCGAATTCACCCTGCCCTGCCCACAG
Seq C2 exon
CTTTCGGCCACGTGGAAACGCGAGCCCATGCGGAGGAGCGCCTCCTGAAGAAACTCTTCTCCGGGTATAACAAGTGGTCCCGTCCCGTCGCCAACATTTCGGATGTGGTCCTGGTCCGCTTCGGCTTGTCCATAGCCCAGCTCATCGATGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005801:ENSGALT00000009316:1
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:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.8=76.5)
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:
TCCTGTATCTCTTGCGAGCGA
R:
GAGTTTCTTCAGGAGGCGCTC
Band lengths:
355-1535
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]