BtaINT0084388 @ bosTau6
Intron Retention
Gene
ENSBTAG00000022635 | LAMC1
Description
Bos taurus laminin, beta 2 (laminin S) (LAMB2), mRNA. [Source:RefSeq mRNA;Acc:NM_001046247]
Coordinates
chr22:51467249-51467813:+
Coord C1 exon
chr22:51467249-51467345
Coord A exon
chr22:51467346-51467440
Coord C2 exon
chr22:51467441-51467813
Length
95 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
TCTGTCCTTTGCCCACACAGCCT
3' ss Score
8.49
Exon sequences
Seq C1 exon
TTCACAGGTCAGTGCCACTGCCGTGCTGGTTTCGGCGGGCGGACCTGTTCTGAGTGCCAGGAGCTCCACTGGGGAGACCCTGGGTTGCAGTGCCGAG
Seq A exon
GTAAGGGGGCTAGAGGGGCCAGAGTAGATGGGGGGGTGCTTCCCAGGATGCTCCACTGGCACCCTGACCCTGTGGTCTGTCCTTTGCCCACACAG
Seq C2 exon
CCTGTGACTGTGACCCTCGTGGGATAGATACACCTCAGTGTCATCGTTCCACGGGCCACTGCAGCTGCCGCCCTGGCGTGTCTGGCGTGCGCTGTGACCAGTGTGCCCGTGGCTTCTCGGGAGTCTTTCCCACCTGCCATCCCTGCCACGCGTGCTTTGGGGACTGGGACCGCGTGGTGCAGGATCTGGCGGCCCGCACACGGCGCCTGGAGCAGTGGACGCAAGAGCTGCAGCAGACGGGCGTGCTGGGTGCCTTTGAGAGCAGTTTCCGGCACCTGCAGGAGAAGCTGGGCACTGTGCAGGGCATCGTGGCTGCCCGAAACGCCTCCGCCGCCTCCACTGCACAGCTCGTGGAGGCCACAAAGGAGCTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000022635:ENSBTAT00000057452:24
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=0.016
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=PD(66.0=93.9)
A:
NA
C2:
PF0005319=Laminin_EGF=WD(100=40.8),PF041117=APG6=PU(51.9=64.8)
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:
TGTTCTGAGTGCCAGGAGCTC
R:
GAAAGACTCCCGAGAAGCCAC
Band lengths:
181-276
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]