GgaINT0011787 @ galGal3
Intron Retention
Gene
ENSGALG00000005321 | LAMA5
Description
NA
Coordinates
chr20:7828970-7829531:-
Coord C1 exon
chr20:7829327-7829531
Coord A exon
chr20:7829115-7829326
Coord C2 exon
chr20:7828970-7829114
Length
212 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGG
5' ss Score
5.85
3' ss Seq
GTCTTTTGCATCCTGCTCAGGTG
3' ss Score
7.91
Exon sequences
Seq C1 exon
CCTGTGACTGTGGGACACGACTCTGCGACGAGGTGACAGGGCAGTGCATCTGCCCTCCTCACACCCTGAAGCCAGAATGTGTTGTCTGTGAGCCCCAGACCTTCGGTTGCCATCCCCTCATCGGCTGTGAGGACTGCAATTGCTCGCAGCCTGGAGTGCAGGAGCTGACAGAGCTTGGCTGTGATGTGGACAGCGGGCAGTGCAA
Seq A exon
GTGAGGAAGCCCTGTCTCTGTGCAGGGCACAGCTGGCAGTATCTCTAGTTGCTGCTGGGGTGATCGGAAACACTGGAAGGGTGCAGGGAGGAAACGGGCAGGATAGGGAAATCCTTGTCAGCACTGTGCGCCTCCCAGCACGGATGAAGCTTTGCAAATGCAGCAGCATAAAGCATAGGTTTCTAATGCTACGTCTTTTGCATCCTGCTCAG
Seq C2 exon
GTGTAAGCCCAATGTAATTGGGCGACGGTGTGACCTCTGTGCCCCTGGCTACTACCACTATCCCAGCTGTCGGCGGTGTGACTGCCATCCTGATGGCACCGAAGTGAGCGTGTGTGACCCGGTGACGGGGCAGTGTCACTGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005321:ENSGALT00000008535:36
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:
PF0005319=Laminin_EGF=PD(6.1=4.3),PF0005319=Laminin_EGF=PU(46.9=33.3)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(51.0=51.0),PF0005319=Laminin_EGF=PU(44.9=44.9)
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:
GACTCTGCGACGAGGTGACAG
R:
CACTTCGGTGCCATCAGGATG
Band lengths:
293-505
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]