DreINT0088143 @ danRer10
Intron Retention
Gene
ENSDARG00000002084 | lamb2
Description
laminin, beta 2 (laminin S) [Source:ZFIN;Acc:ZDB-GENE-081030-4]
Coordinates
chr23:20283544-20283845:-
Coord C1 exon
chr23:20283766-20283845
Coord A exon
chr23:20283680-20283765
Coord C2 exon
chr23:20283544-20283679
Length
86 bp
Sequences
Splice sites
5' ss Seq
CCAGTCAGT
5' ss Score
0.29
3' ss Seq
GTGTCATTAACTGTCTTTAGATG
3' ss Score
6.54
Exon sequences
Seq C1 exon
CCTGAGCACTGGGCCTTGAGTCATGATACCAGTGGCTGCAGAGGGTGTGACTGTGATGTGGGCGGAGCTACAGAAAACCA
Seq A exon
GTCAGTTTTATTCAGACTGTGCGGGGGGGATAAATTTGTTTTAAATGCATAATAATCAATCACATTGTGTCATTAACTGTCTTTAG
Seq C2 exon
ATGCTCAATGGAAACAGGGCAGTGTCAGTGTCGAAGCCACATGATTGGTCGCCAGTGCAACCAGGTGGAGTCTGGGTACTTTTTCATGGCACTTGACCACTACATCTATGAAGCTGAAACTGCCAAACTGGGTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002084:ENSDART00000147326:13
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(24.0=44.4),PF0005319=Laminin_EGF=PU(24.4=40.7)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(73.3=71.7)
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:
GCAGAGGGTGTGACTGTGATG
R:
CCCAGTTTGGCAGTTTCAGCT
Band lengths:
175-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]