DreINT0088026 @ danRer10
Intron Retention
Gene
ENSDARG00000058543 | lama5
Description
laminin, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-030131-9823]
Coordinates
chr23:9732695-9732985:-
Coord C1 exon
chr23:9732933-9732985
Coord A exon
chr23:9732795-9732932
Coord C2 exon
chr23:9732695-9732794
Length
138 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
TGTTGTTTTTGCTTTCTCAGGGC
3' ss Score
10.49
Exon sequences
Seq C1 exon
TGGGGACTTGTAACCCAGCAGGTTCTGTTCATAATGACATTCTACCCACTGTG
Seq A exon
GTAAGTGTTTGTTTCCAATTACTGTACACCTTTTCTATTGTTATTTCTTTCTTAACGCTGTACTTGAGGATCTTGTTGTCTTTTTCAAATATCATTCTTGGTCCAGGCTCTCAGATTTTGTTGTTTTTGCTTTCTCAG
Seq C2 exon
GGCTCTTGTGTGTGTCGGCCGTATGTGGAGGGAGTGGCGTGTGAACGCTGTAAACCTCTCTACTGGAATCTGTCTCCTGATACAATCTATGGATGCTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058543:ENSDART00000045126:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=PD(6.1=16.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGACTTGTAACCCAGCAGG
R:
GCATCCATAGATTGTATCAGGAGACA
Band lengths:
147-285
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]