BtaINT0084389 @ bosTau6
Intron Retention
Gene
ENSBTAG00000022635 | LAMC1
Description
Bos taurus laminin, beta 2 (laminin S) (LAMB2), mRNA. [Source:RefSeq mRNA;Acc:NM_001046247]
Coordinates
chr22:51467441-51468080:+
Coord C1 exon
chr22:51467441-51467813
Coord A exon
chr22:51467814-51467895
Coord C2 exon
chr22:51467896-51468080
Length
82 bp
Sequences
Splice sites
5' ss Seq
GCGGTGCGG
5' ss Score
6.09
3' ss Seq
TTCTGTATCACTTCACACAGGCG
3' ss Score
5.49
Exon sequences
Seq C1 exon
CCTGTGACTGTGACCCTCGTGGGATAGATACACCTCAGTGTCATCGTTCCACGGGCCACTGCAGCTGCCGCCCTGGCGTGTCTGGCGTGCGCTGTGACCAGTGTGCCCGTGGCTTCTCGGGAGTCTTTCCCACCTGCCATCCCTGCCACGCGTGCTTTGGGGACTGGGACCGCGTGGTGCAGGATCTGGCGGCCCGCACACGGCGCCTGGAGCAGTGGACGCAAGAGCTGCAGCAGACGGGCGTGCTGGGTGCCTTTGAGAGCAGTTTCCGGCACCTGCAGGAGAAGCTGGGCACTGTGCAGGGCATCGTGGCTGCCCGAAACGCCTCCGCCGCCTCCACTGCACAGCTCGTGGAGGCCACAAAGGAGCTGCG
Seq A exon
GTGCGGACGAACCCGAGGATGAGTGGTGGGATGGGGCAGGGGCCCAACGCGCCAGGCCTGAATTCTGTATCACTTCACACAG
Seq C2 exon
GCGCGAAATCGGGGAGGCCACGGAGCACCTGACCCGGCTGGAGGCTGAGCTTACAGACGTGCAGGATGACAATTTCAACGCCAACCACGCACTGAGTAGTCTAGAGCGAGACGGGCTTGCACTTAATCTCACGCTGCGGCAGCTTGACCAGCATCTGGACCTGCTCAAGCATTCAAACTTCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000022635:ENSBTAT00000057452:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.016 A=NA C2=0.063
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=WD(100=40.8),PF041117=APG6=PU(51.9=64.8)
A:
NA
C2:
PF041117=APG6=FE(39.7=100)
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:
CTTTGAGAGCAGTTTCCGGCA
R:
CACGTCTGTAAGCTCAGCCTC
Band lengths:
181-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]