BtaINT0084346 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011966 | LAMC1
Description
Bos taurus laminin, gamma 1 (formerly LAMB2) (LAMC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001206817]
Coordinates
chr16:65633026-65633640:+
Coord C1 exon
chr16:65633026-65633215
Coord A exon
chr16:65633216-65633527
Coord C2 exon
chr16:65633528-65633640
Length
312 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
GCCCCTTCCTTTTTCTCTAGGCT
3' ss Score
11.48
Exon sequences
Seq C1 exon
CAAAGTTCTTGGGCAAGCAGGTGTTGAGTTATGGTCAGAATTTCTCCTTCTCCTTCCGCGTGGACAGGCGAGACACTCGCCTCTCGGCAGAAGACCTGGTGCTTGAAGGAGCTGGCATGAGAGTGTCTGTGCCCTTGATTGCTCAGGGCAATTCCTATCCAAGTGAGACCACTGTCAAATATGTCTTCAG
Seq A exon
GTAAGACAGTTCGGTTTATAAAATCTGACTTGACCAGAATTATAAAAGTGGCTTCTTTATCTAAGCGCCTCAGGCCTCAAGGTGTGTATTAAAGAAAAACTTTGGGGTTCTCGATGTGACTTTGTAAAAGGGAACTTTCCCCTTGATTACCTGTACCTTTTCCAGTGGTATGGTCAAACCAACAGACTAATCTCTGACGTGGTTAGACCAGCAGAGCAGTGCATTGTGGGTGGCATGGATGACTAAGAAATACTTTCTCAGCACCCAGAATTGTCCTTACAGAGGTTAACGTGCCCCTTCCTTTTTCTCTAG
Seq C2 exon
GCTCCATGAAGCGACAGATTACCCTTGGAGGCCTACTCTTACCCCTTTCGAATTTCAGAAACTCCTGAACAATTTGACCTCTATCAAGATTCGTGGGACATACAGTGAGAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011966:ENSBTAT00000015881:10
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:
PF0005213=Laminin_B=FE(48.1=100)
A:
NA
C2:
PF0005213=Laminin_B=FE(29.0=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:
CAAAGTTCTTGGGCAAGCAGG
R:
TCTCTCACTGTATGTCCCACGA
Band lengths:
302-614
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development