BtaINT0084909 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030296 | LCNL1
Description
lipocalin-like 1 [Source:HGNC Symbol;Acc:HGNC:34436]
Coordinates
chr11:106245231-106245948:-
Coord C1 exon
chr11:106245809-106245948
Coord A exon
chr11:106245305-106245808
Coord C2 exon
chr11:106245231-106245304
Length
504 bp
Sequences
Splice sites
5' ss Seq
CACGTAAGT
5' ss Score
10.16
3' ss Seq
CGCTGGGGTCCCCTTCCCAGGCC
3' ss Score
7.93
Exon sequences
Seq C1 exon
TTCCAGGGCCCCTGGTACGTGGTTGGGGCGGTGTCGGACGACCAGAGCTTCCTGGATGCCAAGGACAACATGAAGATGCCCGTGGTCTTGGTGACCTCCTTGGCCAACGGCAACCTGGGCATCAAGTTTGGGTTCCCCAC
Seq A exon
GTAAGTGATCCCAGGAGTCCCACCTTGGACTGGCTGGCCTTAGGCCTGGCCAGCTTGGGGTCAGGTGGGAGCCAGGAGGAAGCAGGGGTACGCCCGACCCCAGAGCCAGGCCCGCCCATGCTAGGCTTCAGGGCTGTCGAAACAGCAGCCCCACTCACCTGCTCCTCAGAGGGGCCCCACCTGAGCGTGTGGGGGAGCCATGTCCGTGTGTGTGCGCGCGTATGCACGTGTGCCGGTGTCTCGAGGGGCGACGGGGAGACCCTACAGGCCCCCCGTCCCCTGGCTGTGTCCCTCTGCCCCAGGGTGTCTCCTCTCCTGTAAGTGAATCATAAAGCACCCATGTGATCAAGCGTTGATCTGATGGGAGACAGGTGGCCCTGGGGCAGTTGGCAGCAGCTAAGTGGCAGCTGTTTTTGTCGCGGTCGGGCAGCGTCTTCAGGACACCCAGCAGGGCTGGGCGGTGGGCAGGGGCTGCAACTCAGGCCGCTGGGGTCCCCTTCCCAG
Seq C2 exon
GCCCGATGGCGGGTGCCAGGAGACAGACAGCACCTTCACCAAGGGGACCGTGGACGGGCAGTTCAGCAACGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030296:ENSBTAT00000042776:2
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=0.500
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=PU(31.9=95.7)
A:
NA
C2:
PF0006118=Lipocalin=FE(17.7=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:
CCCCTGGTACGTGGTTGGG
R:
CCTCGTTGCTGAACTGCCC
Band lengths:
206-710
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development