BtaINT0084205 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003061 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:HGNC:6485]
Coordinates
chr13:55417997-55418477:+
Coord C1 exon
chr13:55417997-55418141
Coord A exon
chr13:55418142-55418336
Coord C2 exon
chr13:55418337-55418477
Length
195 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CCGTGCCCTCCCACCCTCAGGAG
3' ss Score
9.78
Exon sequences
Seq C1 exon
GTGCAGACCCAACGTGGCCGGACGCCGCTGTGACACCTGTGCTCCGGGGTTCCATGGCTTCCCCAGCTGCCGCCCCTGTGACTGCCATGAGGCAGGCTCTGCGCCCGGCACGTGTGACCCCCTCACAGGCCAGTGCTACTGCAAG
Seq A exon
GTGAGGGGTCCACTGGCCCGGCCCGCTCCCCACCCCATCCCTCATCTTGCTTTGTCAGCTGAAGTTCATCCTCTCTGGGAGGCTGGGGCCTCCTGGAACACTTTGGGACAGCCAGCTCAGTTGCAGGGTGACAGGCAACACTGGCTGGACCCCCTACACGTGGCTGACTGCCCTGCCGTGCCCTCCCACCCTCAG
Seq C2 exon
GAGAACGTGCAGGGCCCGAGGTGTGACCAGTGCCGCCTGGGGACATTCTCACTGGATGCTGCCAACCCCAAAGGCTGCACCCGCTGCTTCTGCTTCGGGGCCACTGACCGCTGCCGGAGCTCGACGTATGCCCGTCGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003061:ENSBTAT00000003981:36
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=PD(51.0=51.0),PF0005319=Laminin_EGF=PU(44.9=44.9)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(51.0=53.2)
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:
GCTGTGACACCTGTGCTCC
R:
ATACGTCGAGCTCCGGCAG
Band lengths:
248-443
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development