GgaINT0011762 @ galGal3
Intron Retention
Gene
ENSGALG00000005321 | LAMA5
Description
NA
Coordinates
chr20:7848368-7848913:-
Coord C1 exon
chr20:7848779-7848913
Coord A exon
chr20:7848431-7848778
Coord C2 exon
chr20:7848368-7848430
Length
348 bp
Sequences
Splice sites
5' ss Seq
ACCGTAAGT
5' ss Score
10.43
3' ss Seq
ATGTCTCTTTCTCCACGCAGCTG
3' ss Score
10.23
Exon sequences
Seq C1 exon
GTTGCAACTGCAAGTCTGACTTCACTGATGGCACCTGTGAGGACCTCACTGGCCGCTGTTACTGCAAACCCAACTACACCGGGGAGCACTGCAATGCCTGTGCTGAGGGATACCTGGACTTCCCCCACTGCTACC
Seq A exon
GTAAGTACAGCAAGCGAGGCCATGCGGTGGCCAAGTCCAGGATCTCTTAGACTCAACAGGTGCAGGAACGGTCAGGGCTCTGTTTGGGGCTGCTCTCTCTCTTTATCTCACGCCACATTGGCACTCCTGTCCCAGGAGTGGTTCCCACAGGTGTGAATGGGCCTGGGCTTTCTGTGGGTTGAGATGGAACCAGGGGGTCAATGGGAACTTCCTATTTGTCTGATGTTTGATCTCCCACTTTGCGTGCAGGAGGGAAAAAGGCATCATTCAGGAGTCCAGGTTAAGAGTGGCTGTAATTGATTCTTGGTGTGGTGTGGTGACCTGTGCAATGTCTCTTTCTCCACGCAG
Seq C2 exon
CTGTTCCAGCCTTTGCTTATAACGATACTGGAGAACAAGTGCTCCCTGCAGGACAGATAATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005321:ENSGALT00000008535:11
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=PU(93.6=95.7)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(4.3=9.1)
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:
GCAACTGCAAGTCTGACTTCAC
R:
ATTATCTGTCCTGCAGGGAGC
Band lengths:
193-541
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]