DreINT0088025 @ danRer10
Intron Retention
Gene
ENSDARG00000058543 | lama5
Description
laminin, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-030131-9823]
Coordinates
chr23:9732933-9733207:-
Coord C1 exon
chr23:9733070-9733207
Coord A exon
chr23:9732986-9733069
Coord C2 exon
chr23:9732933-9732985
Length
84 bp
Sequences
Splice sites
5' ss Seq
AACGTGAGA
5' ss Score
5.13
3' ss Seq
ATTGTGTTTCTGTACTTTAGTGG
3' ss Score
6.69
Exon sequences
Seq C1 exon
CATGTGATTGCTCAGTGGAGGGCTCTCGCTCCAGCTCCTGTGATCCAGTGTCAGGACAGTGTGTGTGTCTGCCGAACATCGAGGGTCAGAGGTGTGACAGCTGCAGTCCTGGGTCATATGGCTTCCCCCTTTGCCAAC
Seq A exon
GTGAGAGAGACAATCAAATATAATCATGTTTATTAAATTAACATACTTTTGTTCTGATGTTTTTATTGTGTTTCTGTACTTTAG
Seq C2 exon
TGGGGACTTGTAACCCAGCAGGTTCTGTTCATAATGACATTCTACCCACTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058543:ENSDART00000045126:16
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(0.1=0.0),PF0005319=Laminin_EGF=PU(91.8=95.7)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(6.1=16.7)
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:
GATTGCTCAGTGGAGGGCTCT
R:
TTATGAACAGAACCTGCTGGG
Band lengths:
167-251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]