BtaINT0084209 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003061 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:HGNC:6485]
Coordinates
chr13:55394751-55395125:+
Coord C1 exon
chr13:55394751-55394869
Coord A exon
chr13:55394870-55394954
Coord C2 exon
chr13:55394955-55395125
Length
85 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
TGATCTGCGTCCATCCTCAGATC
3' ss Score
9.31
Exon sequences
Seq C1 exon
CCTCCAAGAGGGACTGCCTGGAACGGTTCGGGCTGCGGACGCTGGAGCGCATCACGCAGGACGACGATGTCATCTGCAGCACCGAGTACTCCCGGATTGTGCCTCTGGAGAACGGCGAG
Seq A exon
GTGGGCCGGGCGGGACGGCGTGGGGCATGCGGTCTGGCGGTCAGTGCCGGCACCATGCCCCTGCCTGATCTGCGTCCATCCTCAG
Seq C2 exon
ATCGTGGTGTCCTTGGTGAACGGGCGCCCAGGTGCTATGAACTTCTCCTACTCGCCGCTGCTGCGTGACTTCACCAAAGCCACCAACATCCGCCTGCGCTTCCTGCGCACCAACACGCTGCTGGGCCACCTCATGGGCAAGGCGCTGCGGGACCCCACGGTCACCCGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003061:ENSBTAT00000003981:4
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:
PF0005512=Laminin_N=FE(15.4=100)
A:
NA
C2:
PF0005512=Laminin_N=FE(22.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAAGAGGGACTGCCTGGAA
R:
AGCGGCGAGTAGGAGAAGTTC
Band lengths:
175-260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development