RnoINT0084163 @ rn6
Intron Retention
Gene
ENSRNOG00000002680 | Lamc1
Description
laminin subunit gamma 1 [Source:RGD Symbol;Acc:621052]
Coordinates
chr13:70682307-70683150:-
Coord C1 exon
chr13:70682905-70683150
Coord A exon
chr13:70682461-70682904
Coord C2 exon
chr13:70682307-70682460
Length
444 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGT
5' ss Score
8.54
3' ss Seq
TCTCTGTCTTCCCACCCTAGCCT
3' ss Score
8.61
Exon sequences
Seq C1 exon
GCAAGAGATGTGAGCTCTGTGATGACGGCTACTTTGGAGACCCTCTGGGCAGCAATGGACCCGTGAGACTCTGCCGCCCATGTCAGTGCAACGACAACATAGACCCCAACGCAGTTGGCAACTGCAACCGTCTGACTGGAGAATGCCTGAAGTGCATCTATAACACGGCTGGCTTCTACTGCGACCGGTGCAAAGAAGGGTTTTTCGGAAATCCCCTGGCTCCCAATCCAGCAGACAAGTGCAAAG
Seq A exon
GTTAGTCACTGGCCAGACTCAGTCCCGCGCACGCCTTGATGTGCAGATCCGCCGTGGGGTCTCTTTCAGTGCCTACAGAAGTTTGTGCAGTGTGAACCATTTGCAGAACTTAAAATGGCTGCACTCCGCACCAAAAAAAAAAGTGAAACAGGAGAATTTATTATGTTGACAATGTAGCGGATGTTTTATTGCTTGTTATTATTCAGGTAATAATCAGTTAACAACTCTGAATACGATGGTTCTCTTTTCACCCTGTGTTTACAAAGTCAGTGCATGTTTTAATTGACAGCACATCTCTGTTCAGATTACTAAGACAAGACTCTCTGTGCCTGGGCAGCTTCTGTACGAGACAACGCAGGCCTAAAGAACCTGTTCAAGTGTCTCATGCTTTAGTGCTCTCCCTGGTGATTCGCATCTGTGACTGTCTCTGTCTTCCCACCCTAG
Seq C2 exon
CCTGCGCCTGCAATCCCTATGGTACAGTACAGCAGCAGAGCAGCTGTAACCCAGTGACCGGGCAGTGCCAGTGTCTGCCTCATGTGTCAGGCCGGGACTGTGGCGCTTGTGACCCTGGCTTCTACAACCTGCAGAGCGGGCAAGGCTGCGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002680:ENSRNOT00000003605:14
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(42.3=26.5),PF0005319=Laminin_EGF=WD(100=65.1)
A:
NA
C2:
PF0005319=Laminin_EGF=WD(100=94.2)
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:
CGGCTACTTTGGAGACCCTCT
R:
CTGCAGGTTGTAGAAGCCAGG
Band lengths:
355-799
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]