DreINT0088058 @ danRer10
Intron Retention
Gene
ENSDARG00000058543 | lama5
Description
laminin, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-030131-9823]
Coordinates
chr23:9682039-9682448:-
Coord C1 exon
chr23:9682265-9682448
Coord A exon
chr23:9682180-9682264
Coord C2 exon
chr23:9682039-9682179
Length
85 bp
Sequences
Splice sites
5' ss Seq
GGAGTGAGT
5' ss Score
6.05
3' ss Seq
TTGTGTGTTTGTGTGTGTAGAGT
3' ss Score
7.77
Exon sequences
Seq C1 exon
CATGGGACATTTGGCTTTGATTCCTGCACTGGTTGCAGAAAGTGTGACTGTGATGCGTCAGCTGCGTTGGTTCAGGCATGTGACCCTGTTAACGGCGCATGTGCCTGTCAGCCTGGGGTCAATGGACCGAACTGCCACCAGTGTGCACCTGGTCACTGGAACTACAGTTCTAATGGTTGCAGGA
Seq A exon
GTGAGTCAACATAGCACAAATACATTAAGCTCAAGGGCATATGTTGAATTATGAGTTACATTTATTTGTGTGTTTGTGTGTGTAG
Seq C2 exon
AGTGTGAGTGTAAGGGTGGTCGCTGCGACCCTCGCACAGGAGAGTGTAGATGTACAACAGGTCTGACAGGGAAGCAGTGTGACACGTGTCTCAGTCAGCACAGCGTCCCTGTGCAGAATGGAGCAGATATGCACTGTCAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058543:ENSDART00000045126:47
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(24.4=17.7),PF0005319=Laminin_EGF=PU(92.2=75.8)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(5.9=6.2),PF041569=IncA=PU(8.4=39.6)
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:
TGCACCTGGTCACTGGAACTA
R:
ATCTGCTCCATTCTGCACAGG
Band lengths:
169-254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]