BtaINT0084910 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030296 | LCNL1
Description
lipocalin-like 1 [Source:HGNC Symbol;Acc:HGNC:34436]
Coordinates
chr11:106244989-106245304:-
Coord C1 exon
chr11:106245231-106245304
Coord A exon
chr11:106245100-106245230
Coord C2 exon
chr11:106244989-106245099
Length
131 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
AGGCTCCCACGCGCCCCCAGCTA
3' ss Score
4.56
Exon sequences
Seq C1 exon
GCCCGATGGCGGGTGCCAGGAGACAGACAGCACCTTCACCAAGGGGACCGTGGACGGGCAGTTCAGCAACGAGG
Seq A exon
GTGAGGCCTGCGTGTCGCGGGCAGTGCTGGTCGGGTGGGGGCAGTGGCAGGGCCAGCTCGCGGGGACCGTGGGGATGGGCAGGGGGCGTCCAGGCCGGCGCCCAGCTCAGCAGGCTCCCACGCGCCCCCAG
Seq C2 exon
CTATGGCCCAGACCGACATCAGGGTGGCTTTCACCGACTATAAGCACTTCGCCGTCATGTACTTCGAGACTCAGAAGGGGGGTGTAAAGAACATCTGGCTGCAGCTCTACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030296:ENSBTAT00000042776:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(17.7=100)
A:
NA
C2:
PF0006118=Lipocalin=FE(26.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGGAGACAGACAGCACCTT
R:
CGTAGAGCTGCAGCCAGATG
Band lengths:
170-301
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development