BtaINT0084229 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003061 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:HGNC:6485]
Coordinates
chr13:55426627-55427681:+
Coord C1 exon
chr13:55426627-55426737
Coord A exon
chr13:55426738-55427501
Coord C2 exon
chr13:55427502-55427681
Length
764 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
CTCCACACGGCTCACTGCAGATG
3' ss Score
3.81
Exon sequences
Seq C1 exon
CGCGGGCCACCCTCCAGAACACTGGGACCCAGCTCCGCGATGCCCGGGCCAGGAAGGAGCAGCTGGCGGCCCGTGTCCGGGAGGTGCAAGCCCTGCTGGCTATGGACACAG
Seq A exon
GTAGGGTGGGTCTCCTCCCTGCAGTTCCCCCACCTCTTGTCCCCAGAGCTGAAGGGGCACCTACCCACACGGGCATCACCCCACCAGCCCTGCCTGTCCAGTGGAGTCACCATCCAGGAAGGGGCCCAGGGTAGTTCCAACCCTGGGGACTCTCCCCAGCCCTAAGGACTTGCTTCTGGTCGGGAATCAGACACCAAACAAACGTCACCCCCAACGTCAGCCTGGGTAGCAAGTGAACCCAGGAGGAATGGGGAGCATTTGGAGAGAGAGGACGCGGGGCGGACGGGGAAGGTACAGGTGTTCAGTGGGCTCAGAGATGGCAGCAGCAGCAGGGGTCAGTGTGGCTGGAGCTGGACGCCCAGGAGACACCTCAAGGGTCCAGGGGCCGGGAGGGCTCAGGGCACAGGAGGGATCCCTGCTGACTCGAGAGTGGACCCTGCCTACCAGCCTGGGGGCCATGGGGACTCTGGAAGGACCTCAGGAGAGATGGAGTGGCGGGGGTGGGGGTGGGGGGACTGACCAGGGGGAGATGAGGCTGAGCTGACTCAAGCAGGCCTCAGGGGACTCCACTCAGGTGTGTGGCTGGCACAGGAGGGCTGTCTATCTGGGAGGGGGTGGCGGGTGAGTCTCTACCGCCCTGAGGTTCTCACGAGTCAGGGGGGCGGGGTTAATTCCCTGTTGCTGGTTCTGGCAGGGGGTCTTAGTGGTCTCCCCAGATAAGGATGAGGCCCCTCCCCACTGAGCCTCCACACGGCTCACTGCAG
Seq C2 exon
ATGAGACAAGCAAGAAGATAGCCCATGCCAAGGCCGTGGCCGCTGAGGCCCAGGACACAGCTGCCCGCGTGCAGTCCCAGCTTCAGGACATGCACCGGAACGTCGAGCAGTGGCAGGGCCAGTACAAGGGCCTGCAGAGCCAGGACCTGGGCCGTGTGGTGCTTGATGCTGGCCGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003061:ENSBTAT00000003981:58
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.263 A=NA C2=0.295
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF060097=Laminin_II=PU(38.9=83.6)
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:
CGGGCCACCCTCCAGAAC
R:
GCATCAAGCACCACACGGC
Band lengths:
278-1042
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development