DreINT0088036 @ danRer10
Intron Retention
Gene
ENSDARG00000058543 | lama5
Description
laminin, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-030131-9823]
Coordinates
chr23:9716047-9716528:-
Coord C1 exon
chr23:9716375-9716528
Coord A exon
chr23:9716211-9716374
Coord C2 exon
chr23:9716047-9716210
Length
164 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGC
5' ss Score
4.72
3' ss Seq
TACAATATAATTGTGTTCAGATC
3' ss Score
5.51
Exon sequences
Seq C1 exon
CTGTCTGCAGTACATGTATCTGTCTCTGGATGAGTTCCCATCCATCTCCAGCAATGATGCCAGCTGCAGGTCTGATAATCACCTGCCCAGACCCTGCCACACTGAAAAGATCACGCCTCGCCATCCCAGCATGGCCATCTGCAGCGGCAATGAT
Seq A exon
GTGAGCATGTGCACACACATGATGAAACAACACAGTCAAATGTAGATAGAGTAAGGAAAATCTTAAAATACACAAGTTTAGGGTCAATCAGGGTTTTTTTCCGGAAGTGATTGAGAGTGTGTGCATGCATTTGTGTTGAAAACGTACAATATAATTGTGTTCAG
Seq C2 exon
ATCAGCGTTGGGCTGCGTGGTCGAGTTCCTGTTCCTGGAGAGTATGTGTTAGTGGTAGAATACGCCAGTGAAGATCAAGCCCCTCAAAACCTTACAGTGTCTGTCAGCTCAGCAGGTGAATCCACTCATCAGGAGCAAATAACACTGCTCCACTGCAAATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058543:ENSDART00000045126:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.096 A=NA C2=0.127
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
AGTTCCCATCCATCTCCAGCA
R:
GGATTCACCTGCTGAGCTGAC
Band lengths:
245-409
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]