BtaINT0084350 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011966 | LAMC1
Description
Bos taurus laminin, gamma 1 (formerly LAMB2) (LAMC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001206817]
Coordinates
chr16:65643591-65644451:+
Coord C1 exon
chr16:65643591-65643836
Coord A exon
chr16:65643837-65644297
Coord C2 exon
chr16:65644298-65644451
Length
461 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACC
5' ss Score
8.55
3' ss Seq
TCTGTGTCTTCCTTCCGTAGCCT
3' ss Score
10.75
Exon sequences
Seq C1 exon
GTAGAAGGTGTGAGCTCTGTGATGACGGCCACTTTGGAGACCCTCTGGGTAGCAACGGCCCCGTGAGGCTTTGCCGCCTGTGTCAGTGCAATGACAACATCGATCCCAACGCTGTTGGGAATTGCAACCGCCTGACGGGAGAATGCCTGAAGTGCATCTATAACACGGCCGGCTTCTACTGTGACCGGTGCAAAGATGGATTTTTTGGAAATCCCCTGGCTCCCAATCCAGCAGACAAATGCAGAG
Seq A exon
GTAACCAGCCATCGGCCACATCCTCTCGCAGTTACACTTACACATCCTGAGCGTCACTGCACGGTCTCTTTAAATATTTACAGTTGTCTGGTCTAATGCAGCGTTGTTCCATAGAGGTATAGCGTGAACCACTTACGTAATTTAAATTATTCTAGTGGATACAGTACAATAAAGAGAAGCAGGTAACGTTACTTTTAACATTGTTTTTTATTTGACATGTCTAACGTATTATCATCTCAGCAAGTAATCAATAAAAAATGCTTGAGAGGTACGTTCTTTTTTTCCCACACTGCTTCTTCAAAGTCGAGTGTGTGTTTCACGTTGACAGCGCATCTCCGTTCGGTGACCGGTGGCTGCTATATTGGACAGCACAAGTCGAAAGACTCTATTTGTGTCGTTTACACTTGAGGGCTCCTCTCGGGTGATGCGCATCTTTTGCTGTCTGTGTCTTCCTTCCGTAG
Seq C2 exon
CCTGTGACTGCAACCCCTACGGGACGGTGAAGCAGCAGAGCAGCTGTAACCCTGTGACCGGGCAGTGCGAGTGTCTGCCCCACGTGACCGGCCGGGACTGCGGCGCTTGTGACCCCGGATTCTACAACCTGCAGAGCGGGCAGGGCTGTGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011966:ENSBTAT00000015881:14
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:
PF0005319=Laminin_EGF=PD(37.7=24.1),PF0005319=Laminin_EGF=WD(100=65.1)
A:
NA
C2:
PF0005319=Laminin_EGF=WD(100=94.2)
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:
TCTGTGATGACGGCCACTTTG
R:
GTAGAATCCGGGGTCACAAGC
Band lengths:
356-817
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development