BtaINT0084216 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003061 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:HGNC:6485]
Coordinates
chr13:55421961-55422430:+
Coord C1 exon
chr13:55421961-55422061
Coord A exon
chr13:55422062-55422249
Coord C2 exon
chr13:55422250-55422430
Length
188 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGCA
5' ss Score
6.37
3' ss Seq
ACTGCAGTCTGTGCCCCCAGGAA
3' ss Score
7.56
Exon sequences
Seq C1 exon
GGTGTGACTGCTCCCCATGCGGGACAGAGGCCTGTGACCCCCACAGTGGACACTGCCTGTGCAAGGCCGGTGTGACTGGGCTGCGCTGTGACCGCTGTCAG
Seq A exon
GTAGCACTGCCTGGGAGGGGCAGGACCTTGATGTAGGGGCGGGGCTCGGTAGGAGGGGGGGAGTTTGTGGGTGGGGCTCAGGGTGATAGGGGCGGGGCTTTGTGTGGGTGGGGCCTCATGGCTCCAGGGCTGAAGGAAGGTGAATTTTGAGGGTTGGGCAGAGCCGTGACTGCAGTCTGTGCCCCCAG
Seq C2 exon
GAAGGACACTTTGGCTTCGAGGGCTGCGAGGGCTGCCGCCCATGCGCCTGTGGACCAGCCGCCGAGAGTTCCGAGTGCCACCCCCAAAGTGGGCAGTGCCACTGCCGGCCAGGGACTGGGGGACCCCAGTGTCGCGAGTGTGCCCCCGGCCACTGGGGGCTCCCCGAGCAGGGCTGCAGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003061:ENSBTAT00000003981:46
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(95.8=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:
GTGTGACTGCTCCCCATGC
R:
CACACTCGCGACACTGGG
Band lengths:
242-430
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development