RnoINT0084033 @ rn6
Intron Retention
Gene
ENSRNOG00000053691 | Lama5
Description
laminin subunit alpha 5 [Source:RGD Symbol;Acc:621023]
Coordinates
chr3:175563167-175563701:-
Coord C1 exon
chr3:175563601-175563701
Coord A exon
chr3:175563348-175563600
Coord C2 exon
chr3:175563167-175563347
Length
253 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGG
5' ss Score
4.44
3' ss Seq
GACGAAGAGGTGTATTACAGGAA
3' ss Score
-2.73
Exon sequences
Seq C1 exon
GGTGTGACTGTTCCCCATGCGGGACAGAAACCTGTGATCCCCAGACTGGGCGCTGCCTGTGTAAGGCAGGCGTGACTGGACAACGTTGTGACCACTGTTTG
Seq A exon
GTAGGGCTGGGTGTAGGCCTGAGGGCGGGGTGGACTAGAGGAAGGAACCAGGCCTGTGGAGAAAGTGTACTGAGAGAGAAGAGTCCTGGTCTGTGGAGAAATGGGCTATGGGGGGAGCTTTAGCTGGTCCTGAGGAGCCTGAGATAGCCCAGGGCTGGCAAAGTGAGCCTGAGATAGCCCAGGTTTCTATCTCAGGGCTGGCAAAGTGTGATGCTGAGGGTTGGGCAGACTGTGACGAAGAGGTGTATTACAG
Seq C2 exon
GAAGGACACTTCGGTTTTGAGCAATGCCAGGGCTGCCACCCTTGTGCCTGTGGACCAGCTGCTGAGGGCTCTGAGTGCAACCCTCAGACTGGTCAGTGTCACTGCCGGCCAGGGACCACAGGACCCCAGTGCCTTGAGTGTGCTCCTGGCTACTGGGGACTCCCGGAGAAAGGTTGCAGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053691:ENSRNOT00000081226:46
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=PU(71.1=94.1)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(24.4=18.0),PF0005319=Laminin_EGF=PU(92.0=75.4)
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:
GGTGTGACTGTTCCCCATGC
R:
AACCTTTCTCCGGGAGTCCC
Band lengths:
276-529
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]