RnoINT0084021 @ rn6
Intron Retention
Gene
ENSRNOG00000053691 | Lama5
Description
laminin subunit alpha 5 [Source:RGD Symbol;Acc:621023]
Coordinates
chr3:175567917-175568434:-
Coord C1 exon
chr3:175568230-175568434
Coord A exon
chr3:175568062-175568229
Coord C2 exon
chr3:175567917-175568061
Length
168 bp
Sequences
Splice sites
5' ss Seq
CAGGCGAGT
5' ss Score
2.92
3' ss Seq
CAGAGTCTTTGTCCTCACAGATG
3' ss Score
7.81
Exon sequences
Seq C1 exon
CCTGTGACTGCGGAGCCCGCCTGTGTGACGAGCTCACAGGTCAGTGTATCTGTCCTCCACGCACTGTGCCCCCCGACTGCCTGGTCTGCCAGCCACAGAGCTTTGGTTGCCACCCCTTGGTGGGCTGTGAGGAGTGTAACTGCTCAGGACCCGGCGTCCAGGAGCTGACGGACCCCACCTGTGACATGGACAGCGGCCAGTGCAG
Seq A exon
GCGAGTCCAGACAGCACCCCACAATCTTGCGGGATCTCGGGTCAGGGAGAGGATCACCTCTCACACCCCACTCCTGTTCATCTCAGATGACACTGTAGGGGCCGGGGTCCTGTGGGATCTGCATGACCCAGGGCTAGAGGGGGACTCACAGAGTCTTTGTCCTCACAG
Seq C2 exon
ATGCAGACCCAATGTAGCTGGGCGTCGCTGTGACACCTGTGCACCAGGCTTCTATAGTTATCCTAGCTGTCGCCCCTGTGACTGTCATGAGGCAGGCACCATGGCCAGTGTGTGTGACCCCTTCACAGGCCAGTGCCATTGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053691:ENSRNOT00000081226:35
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=4.3),PF0005319=Laminin_EGF=PU(46.9=33.3)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(51.0=51.0),PF0005319=Laminin_EGF=PU(44.9=44.9)
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:
TATCTGTCCTCCACGCACTGT
R:
CTGCCTCATGACAGTCACAGG
Band lengths:
254-422
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]