DreINT0088090 @ danRer10
Intron Retention
Gene
ENSDARG00000058543 | lama5
Description
laminin, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-030131-9823]
Coordinates
chr23:9639635-9639999:-
Coord C1 exon
chr23:9639852-9639999
Coord A exon
chr23:9639766-9639851
Coord C2 exon
chr23:9639635-9639765
Length
86 bp
Sequences
Splice sites
5' ss Seq
TCGGTCAGC
5' ss Score
4.32
3' ss Seq
ACTGTGTCTCTGCTCTTTAGACG
3' ss Score
8.02
Exon sequences
Seq C1 exon
GCTGGATTCGTGGGCTGTGTTCGGGACCTGAAACTGAACGAGGTGTCTCTTCAGAGCCCATCTGTCAGTGTAGGTGTGACGCCCTGTTACCAGCAGCCTTTGCAGCCCGGCGCTCACTTCTCCAGTCGTGGAGGATTCATGACCATCG
Seq A exon
GTCAGCCATTTTAATCCTATTATCATACTCTCAGCAGGAACTTTGTGATACACAAACTCTTTGTTCACTGTGTCTCTGCTCTTTAG
Seq C2 exon
ACGAGTCGCTGGTTTTAGGACAGGACCTGGAGATCCAATTGGAGGTCCGTCTGGATTCAGGCTCAGGGCTTCTGCTGCACACTGGAGCCAAGAAAACACACCAGCTGAGTGTGTATCTGGAACAAGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058543:ENSDART00000045126:76
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:
PF0221019=Laminin_G_2=PD(11.6=28.0)
A:
NA
C2:
PF0221019=Laminin_G_2=PU(22.0=63.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGTCAGTGTAGGTGTGACGC
R:
TTTCTTGGCTCCAGTGTGCAG
Band lengths:
182-268
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]