GgaINT0124032 @ galGal4
Intron Retention
Gene
ENSGALG00000003852 | LAMC3
Description
laminin, gamma 3 [Source:HGNC Symbol;Acc:HGNC:6494]
Coordinates
chr17:6076401-6076832:+
Coord C1 exon
chr17:6076401-6076600
Coord A exon
chr17:6076601-6076685
Coord C2 exon
chr17:6076686-6076832
Length
85 bp
Sequences
Splice sites
5' ss Seq
AAGGTCTGA
5' ss Score
4.3
3' ss Seq
CCCACCTCTGTCATTGGCAGAGG
3' ss Score
7.39
Exon sequences
Seq C1 exon
GCATGAGGAAGGTGTTGGGGCATCGGAAAGGTCGTGCTGCCCTGAGAAGGAGAATGGCACAAGTGCGGGACAGAGCAATGGTGGAGGCCCAGAAGAAGATTAAACAGGCAGAGAAAATGCTGGGAAACTCCTTGTCTGTCTCCAGTGCGGCCAGGAGGAAGGCAGGGGAGGCTGTGCATGTTGCTGGGGAGAGCAGTAAG
Seq A exon
GTCTGAGCAGTGGGATGGGGGTGCGGGGAGCAGGACCCCAGCTGCCGTCTGCTGGGGTGACTGTCCCCACCTCTGTCATTGGCAG
Seq C2 exon
AGGGCCCAGGCTGTACTGCAGGGCAGCAAGCAGGCTCGCAAGCACACCAGGACGCTCGCCACACGTGTCAGCGAGACCCAGCAGGAGCTGTACCGGCAGCAGCGCGTGGCTGAGGAGCTCAGGGGGAGCCTGGAGGAGGCAGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003852:ENSGALT00000006123:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.672 A=NA C2=0.755
Domain overlap (PFAM):
C1:
PF102344=Cluap1=PU(26.6=62.7)
A:
NA
C2:
PF102344=Cluap1=FE(30.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGGCAGAGAAAATGCTGGG
R:
GTCTCGCTGACACGTGTGG
Band lengths:
174-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]