BtaINT0084376 @ bosTau6
Intron Retention
Gene
ENSBTAG00000022635 | LAMC1
Description
Bos taurus laminin, beta 2 (laminin S) (LAMB2), mRNA. [Source:RefSeq mRNA;Acc:NM_001046247]
Coordinates
chr22:51460213-51460514:+
Coord C1 exon
chr22:51460213-51460292
Coord A exon
chr22:51460293-51460381
Coord C2 exon
chr22:51460382-51460514
Length
89 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
AGTAACCACGTGTTCCCCAGGTG
3' ss Score
6.47
Exon sequences
Seq C1 exon
CCTGGCCACTGGGGGCTGAGCCACGACCTGCTCGGCTGCCGTCCATGTGACTGCGACATCGGTGGTGCCTTGGATCCCCA
Seq A exon
GTGAGTGCTGTATAAGGGGCCCTGGGTGGTTGGGGAGAGGATCCTGGGCAGGAGGGCGGGATCCTCTGGAGTAACCACGTGTTCCCCAG
Seq C2 exon
GTGCAACGAGGCCACGGGTCAGTGCCGCTGCCGCCAGCACATGGTGGGGCGACGCTGCGAGCAGGTGCAGCCTGGTTATTTCCGGCCCTTCCTTGACCACCTAACTTGGGAGGCTGAGGAACCCCGGGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000022635:ENSBTAT00000057452:13
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(24.0=44.4),PF0005319=Laminin_EGF=PU(24.4=40.7)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(73.3=73.3)
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:
GGCTGCCGTCCATGTGAC
R:
TCCTCAGCCTCCCAAGTTAGG
Band lengths:
167-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]