RnoINT0084164 @ rn6
Intron Retention
Gene
ENSRNOG00000002680 | Lamc1
Description
laminin subunit gamma 1 [Source:RGD Symbol;Acc:621052]
Coordinates
chr13:70681690-70682460:-
Coord C1 exon
chr13:70682307-70682460
Coord A exon
chr13:70681833-70682306
Coord C2 exon
chr13:70681690-70681832
Length
474 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
AGAAATGTGTTTCCTTTCAGTTG
3' ss Score
8
Exon sequences
Seq C1 exon
CCTGCGCCTGCAATCCCTATGGTACAGTACAGCAGCAGAGCAGCTGTAACCCAGTGACCGGGCAGTGCCAGTGTCTGCCTCATGTGTCAGGCCGGGACTGTGGCGCTTGTGACCCTGGCTTCTACAACCTGCAGAGCGGGCAAGGCTGCGAGAG
Seq A exon
GTGAGTCTTGAGTCTGTGGAAAGTGCTCCTTGCTGTCTGGGTCGTAAGAAGTACATCTTTCCAAGTCACTCTGTATTGATAGCTGGCTTGGTGAAGTTTAGGGATGGTTTCCAGTGTCTTATGCAGGAAAGACCATGTTAGAGGTTTTAAGTAGGGGACAGAAGGGATAGCACAGTGGCAGTCCTGGTGTGTCAGACACTTCAAAATACAGATTGCAAAGTTTCTTCCGAGACATACTCATCAGGGCTTCAGCCTGGGAATCTATCTGTCTGGTTTTTGGTCAATAGGGTTTAGTATGGAGGTTGCTGGTATAGGCGAGGCTTGACAAAGAGCTCTGAATAGCACTCACAGAAAGTGCCTGGATGTAAGGGAGCGGCCCTTAACATTCCGACTAAGTCCTTAATGTGCTGCCTTTCGGTAGAGAACGTTGCTTACGCTCTGCTCCTCTTACCCCAGAAATGTGTTTCCTTTCAG
Seq C2 exon
TTGTGACTGCCATGCTTTGGGCTCCACCAACGGGCAATGTGACATCCGCACCGGGCAGTGTGAGTGTCAGCCCGGCATCACCGGTCAGCACTGTGAGCGCTGTGAGACCAACCACTTTGGGTTTGGACCTGAAGGCTGCAAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002680:ENSRNOT00000003605:15
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=WD(100=94.2)
A:
NA
C2:
PF0005319=Laminin_EGF=WD(100=93.9)
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:
GCGCCTGCAATCCCTATGGTA
R:
GTTTGCAGCCTTCAGGTCCAA
Band lengths:
294-768
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]