BtaINT0084211 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003061 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:HGNC:6485]
Coordinates
chr13:55419705-55420588:+
Coord C1 exon
chr13:55419705-55419935
Coord A exon
chr13:55419936-55420474
Coord C2 exon
chr13:55420475-55420588
Length
539 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CCAATGCCCACCCACTCCAGGAG
3' ss Score
5.32
Exon sequences
Seq C1 exon
GGGAACTTCCGACACATGGAGACCCACAGTACTGTGTCCCGCGAGGAGCTCATGATGGTGCTAGCTGGCCTGGAGCAGCTGCATATCCGTGCCCTCTTCTCGCAGGCCTCCTCGGCCGTCTCCCTGCGCAGGGTGGCGCTGGAGGTGGCCAGCGAGATGGGTGGGGGGCCTCCAGCCAGCAATGTGGAGCTATGCATGTGCCCTGCCAACTACCTTGGGGACTCGTGCCAG
Seq A exon
GTGAGGCAGTGGAGGTGGGCACCAGGGCCAAGTGGTCCCCCACCCCGGCCCGCACGTCCCCAGGCATCCACACTTGGCCTCTGTCTCCACCTCACCCCACTTCTCCTCTTATACCTGCTGGGCATCACCCTGCTAGCAGCCGGCCTTCCCGCCTCAGGCCGAGCCGGCTGCTTGTTCGACCATCTGCTCGTCCACCGTCAGCTACTCCCTGCCGGCCCCCGTGTGCCCTAGCTGGTCTTCACGCATTTAGTGCCCAGTTCCCCTTACATCCACAGTTCACCCAGAGAGCATCCACTTCACCTCCTCCCCATCTCACCTGTGGGCCATCCCTCCACCCACTTGGAAGTGTCTAGAGGAGAATGGTGGGTGGGGGTGCCCTGAGCCAGGGCCTCTGTGTGGCTTTGTGGGCTCTGACTTCACGCCTTCAGCCCGTCAGGGTCAGGACCCCTAGGGCTGACCTGTGAGTATGGTCCCTGGTCTGCCCCCACATCAGGCTGGCCCTGCCTCCTTCCCTGACCACCAATGCCCACCCACTCCAG
Seq C2 exon
GAGTGTGCCCCTGGCTATTACCGGGACGTCAAAGGTCTCTTCCTGGGTCGCTGCATCCCCTGTCAGTGCCACGGCCACTCAGACCGCTGCCTCCCTGGCTCAGGCGTCTGTATA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003061:ENSBTAT00000003981:41
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005213=Laminin_B=PD(45.3=80.5),PF0005319=Laminin_EGF=PU(50.0=22.1)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(44.1=39.5),PF0005319=Laminin_EGF=PU(35.4=44.7)
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:
GGGAACTTCCGACACATGGAG
R:
TATACAGACGCCTGAGCCAG
Band lengths:
345-884
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development