GgaINT0001716 @ galGal3
Intron Retention
Gene
ENSGALG00000013419 | PBX4
Description
NA
Coordinates
chrUn_random:30306442-30307041:-
Coord C1 exon
chrUn_random:30306851-30307041
Coord A exon
chrUn_random:30306578-30306850
Coord C2 exon
chrUn_random:30306442-30306577
Length
273 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
TAATGGTGTTTTTTTCACAGGCG
3' ss Score
8.04
Exon sequences
Seq C1 exon
GCCTGCAGCGAGTTCACCACCCACGTCATGAACCTGCTCAGGGAACAGAGCCGGACGAGGCCCATTTCTCCCAAAGAAATCGAGCGGATGGTGAACATCATCCACGGCAAATTCAGCACCATTCAGATGCAGCTGAAGCAGAGCACGTGCGAGGCGGTGATGATCCTCCGCTCACGCTTCCTCGATGCAAG
Seq A exon
GTATGATGAAGAGTGGCAACGGGTGCTCCCATCCGGGCTTCATTTGTTGCTCAGTGCCAGTAATCGCATAGGAAACCTCACTCCCATTGCTGCTAGTTTCCATATTGACAACCCATTGGATGTTGCATGCGCTGAGGCCTCTCACCTTGAGATAAAACGTACCAAAACTGCGTGGAGTTAAATATATTCTTCCTCCAACCAGATATACGTTAGAGTAGGCCCACGGTTCATGTCCACGTGGTGCAAATGGGAATAATGGTGTTTTTTTCACAG
Seq C2 exon
GCGTAAACGGCGTAACTTCAGCAAGCAGGCAACAGAAGTGCTGAATGAGTATTTCTATTCGCACCTGAGCAACCCTTACCCCAGCGAAGAGGCCAAAGAGGAGCTCGCAAAGAAGGGTGGCATCACCGTTTCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013419:ENSGALT00000021886:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.219 A=NA C2=0.196
Domain overlap (PFAM):
C1:
PF037928=PBC=PD(31.3=95.3),PF070286=DUF1319=PD(54.3=79.7),PF040917=Sec15=PD(53.8=54.7),PF0004624=Homeobox=PU(0.1=0.0)
A:
NA
C2:
PF0004624=Homeobox=PU(75.0=97.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCACCACCCACGTCATGAAC
R:
TCTTTGCGAGCTCCTCTTTGG
Band lengths:
292-565
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]