DreINT0088126 @ danRer10
Intron Retention
Gene
ENSDARG00000045524 | lamb1b
Description
laminin, beta 1b [Source:ZFIN;Acc:ZDB-GENE-041210-197]
Coordinates
chr4:25756379-25756947:+
Coord C1 exon
chr4:25756379-25756475
Coord A exon
chr4:25756476-25756809
Coord C2 exon
chr4:25756810-25756947
Length
334 bp
Sequences
Splice sites
5' ss Seq
GATGTGATA
5' ss Score
-6.73
3' ss Seq
GTGTTTCCTGCAGGTGTCAGACG
3' ss Score
-3.25
Exon sequences
Seq C1 exon
GTGTGTGGAGGGGCTGCAGGTCTAGATGGATGTAAGGATTGTGGTGGTCTGGGCTGTAAGCATGAGGATGGCATGTCCCATTGTGGTGGGGAAGGAT
Seq A exon
GTGATACTATTGTGACCCGATCCCAAGACTCCTTAAATAAAGCCAAAAACTTAGACCAGGAGGTCCTGCACACTCTCAAAGAAGTAGACAAGTTAAACAGGATGGCAAGTACACAAACACATTAACTATTCTTATTTATTAATGAAGATCAATATGCTTTGAATCACAGTAATACATTTTTAGATATAAACTTTTATTTATTTTTAATTGATGTTTAAAATAAATAAATACAGCCTTGATAAACTTGAAAAAAGTACAATTATAATCAACTTTACATCAAATTCAACACTGCAAGCGTTTCTAAGGACATGAATGTGTTTCCTGCAGGTGTCAG
Seq C2 exon
ACGCTCGAGGACGTGCGGATGAGGCTAAACTTAGCGCTCAGGATGTGTTACTAAGAGCCAATCAGAGCAAAGCACGAGTGGAACAGACCAATGAGGATCTCAGAAACCTCATTCAGCAGATACGAGACTTCCTCACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000045524:ENSDART00000141133:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.151 A=NA C2=0.405
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGTGGAGGGGCTGCAG
R:
TGTGAGGAAGTCTCGTATCTGCT
Band lengths:
233-567
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]