DreINT0088047 @ danRer10
Intron Retention
Gene
ENSDARG00000058543 | lama5
Description
laminin, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-030131-9823]
Coordinates
chr23:9696527-9696910:-
Coord C1 exon
chr23:9696766-9696910
Coord A exon
chr23:9696668-9696765
Coord C2 exon
chr23:9696527-9696667
Length
98 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTCT
5' ss Score
2.57
3' ss Seq
TGATGTTTGGTCTCTTTCAGGAA
3' ss Score
11.16
Exon sequences
Seq C1 exon
GTGCAGGAACAACATTGTTGGCCGTCAGTGTGACAGGTGTTCTCCAGGTTTCTATGGTTACCCCAACTGCAGGCCATGTAACTGCAATGAGGCGGGAACTGAGATGAATGTTTGCGACTCCTTCACTGGACGCTGTCTGTGCAAG
Seq A exon
GTGTCTTTTCCTCTCCTTCTGCCCCATTATTTTTTATGTCTGTTTTCACTCAGACAATTGATCATCTTTGTTATATATTGATGTTTGGTCTCTTTCAG
Seq C2 exon
GAAAATGTGGAAGGCCCTCGCTGTGACCAGTGCAAACTGGGAACGTTTCATCTGGACCCCACTAATGCTAAAGGCTGCACCAAGTGCTTTTGCTTTGGAGCCACTGATCGCTGCCACAGCTCTGACAAACGCCGAAGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058543:ENSDART00000045126:36
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(52.1=51.0),PF0005319=Laminin_EGF=PU(44.9=44.9)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(51.0=53.2)
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:
TGTGACAGGTGTTCTCCAGGT
R:
GGGTCCAGATGAAACGTTCCC
Band lengths:
176-274
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]