RnoINT0084001 @ rn6
Intron Retention
Gene
ENSRNOG00000053691 | Lama5
Description
laminin subunit alpha 5 [Source:RGD Symbol;Acc:621023]
Coordinates
chr3:175574207-175574601:-
Coord C1 exon
chr3:175574549-175574601
Coord A exon
chr3:175574313-175574548
Coord C2 exon
chr3:175574207-175574312
Length
236 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
ATAGTTTTACTCTCTCCCAGGCA
3' ss Score
7.46
Exon sequences
Seq C1 exon
CTGGCTCTTGTCATCCTGCTGGTCTGGCCCCAGCCAATCCTGCCCTTCCTGAG
Seq A exon
GTAAGTACAGGATTGCCCATGGTGGAGGATTAGGTAGGGGACCCAACCTGCCAAGTCTGAAGTCCAGAGGAACCCTGGTCTCCGTCCGGCCTGCTGCTCGCTTGCTGTGGCAACCTCAGGGCCCAATTGATTCTTCTGCTGGTCCTTTATTTCCATCCTGGGTGGCTGCCAAGCATGGGGTAAGGGCGGGTGAGGGGCTTCAGCCCCCTTTGTCCCATAGTTTTACTCTCTCCCAG
Seq C2 exon
GCACAGGCTCCCTGTACGTGCCGGGCTCATGTGGAGGGGCCAAGCTGTGACCGCTGTAAACCTGGGTATTGGGGACTGAGCTCCAGCAACCCTGAAGGCTGCACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053691:ENSRNOT00000081226:17
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(6.1=16.7)
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:
GCTCTTGTCATCCTGCTGGTC
R:
GTGTGCAGCCTTCAGGGTTG
Band lengths:
156-392
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]