BtaINT0084189 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003061 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:HGNC:6485]
Coordinates
chr13:55409127-55409741:+
Coord C1 exon
chr13:55409127-55409232
Coord A exon
chr13:55409233-55409641
Coord C2 exon
chr13:55409642-55409741
Length
409 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGG
5' ss Score
4.69
3' ss Seq
CACTCACTCCCCCATTGCAGGCT
3' ss Score
8.78
Exon sequences
Seq C1 exon
GGCAACGGCCAGTGCTTCTGCAAGCCCCACGTGTGTGGCCAGACCTGCGCGGCCTGCAAGGACGGCTTCTTCGGGCTGGACCAGGCTGACTACTTCGGCTGCCGCA
Seq A exon
GTAAGGCCCACTGCTTGGCCCTTGGACCACGTCCCGGAGAGGCTGAGGCCCAGGGAGGGACACATGGGACAAGGGCAGCCAGGGCCTGGGTGTCACATGGCACTCGCTGAGCCACTCTGGGTACCTGGCCAGACCTGTGCTGGTGTGGAGGGGGTGCGGATTTAACCCCTTCTTCTCCCTCCATCCCATGCCCTGGCAGGCGTCACTCACCAATCCCAGGGCCCTTGCCCTAAATCCTGACCCTCTGCTGTCCAGAGCCCCGGGCAGCTCCTGGTGGCAGTAACACTTGTCCTCTCAGCCTGGGTCACCCTTGATGGAGGGTGGACGAAGCAGAGTCCTGAGCTGCGGGCTGCGGGAGGAGCATGGAGACCGTGGGGCTGGGCCTCACTCACTCACTCCCCCATTGCAG
Seq C2 exon
GCTGCCGGTGTGATGTTGGCGGAGCGCTGGGGCAGAGCTGTGAGCTGAGGACGGGTGCCTGCATGTGCCGCCCCAACACCCAGGGCTCCACCTGCAGCGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003061:ENSBTAT00000003981:20
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(64.7=91.7)
A:
NA
C2:
PF0005319=Laminin_EGF=PU(72.7=94.1)
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:
GCAACGGCCAGTGCTTCT
R:
CAGGTGGAGCCCTGGGTG
Band lengths:
199-608
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development