DreINT0088057 @ danRer10
Intron Retention
Gene
ENSDARG00000058543 | lama5
Description
laminin, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-030131-9823]
Coordinates
chr23:9682265-9682629:-
Coord C1 exon
chr23:9682529-9682629
Coord A exon
chr23:9682449-9682528
Coord C2 exon
chr23:9682265-9682448
Length
80 bp
Sequences
Splice sites
5' ss Seq
GAGGTGTGT
5' ss Score
6.14
3' ss Seq
TGTTGCTGTTGTGTGTTTAGCAT
3' ss Score
8.04
Exon sequences
Seq C1 exon
GATGCAACTGTTCTCCTTGTGGCACTGCACATTGCGACTCTCACACTGGCCAGTGCCACTGCAAGCCGGGTGTGGTGGGAGCCCAGTGTGATCGCTGTGAG
Seq A exon
GTGTGTGTGCTTGGATGTTCTGTCTATGTATTGGTTTGGTTCAGTGGTAATAGCGTTTTTTGTTGCTGTTGTGTGTTTAG
Seq C2 exon
CATGGGACATTTGGCTTTGATTCCTGCACTGGTTGCAGAAAGTGTGACTGTGATGCGTCAGCTGCGTTGGTTCAGGCATGTGACCCTGTTAACGGCGCATGTGCCTGTCAGCCTGGGGTCAATGGACCGAACTGCCACCAGTGTGCACCTGGTCACTGGAACTACAGTTCTAATGGTTGCAGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058543:ENSDART00000045126:46
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(71.1=94.1)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(24.4=17.7),PF0005319=Laminin_EGF=PU(92.2=75.8)
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:
GCACATTGCGACTCTCACACT
R:
CGTTAACAGGGTCACATGCCT
Band lengths:
169-249
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]