BtaINT0084911 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030296 | LCNL1
Description
lipocalin-like 1 [Source:HGNC Symbol;Acc:HGNC:34436]
Coordinates
chr11:106244630-106245099:-
Coord C1 exon
chr11:106244989-106245099
Coord A exon
chr11:106244732-106244988
Coord C2 exon
chr11:106244630-106244731
Length
257 bp
Sequences
Splice sites
5' ss Seq
ACGGTGGGT
5' ss Score
8.27
3' ss Seq
CACCGCGCCCCTGCTCTCAGCCC
3' ss Score
6.39
Exon sequences
Seq C1 exon
CTATGGCCCAGACCGACATCAGGGTGGCTTTCACCGACTATAAGCACTTCGCCGTCATGTACTTCGAGACTCAGAAGGGGGGTGTAAAGAACATCTGGCTGCAGCTCTACG
Seq A exon
GTGGGTGACACGTGGTGGGAGACCTACCCACCTGAAGAGCCGCACTCACACCACCCTGGCCCCATCGCGGCCTTCCTCTGGGGTCACACGGGAGGTCTGGTCTGCGGTGTCCCCGTGTGCCTTCCCAGCCAGCCCCGACTGGGAGGCAGGTGAAACCAGCATCTCCCCGTGTCTCCCTGGGCCCCTCCCCAGCCCCGCCCCACCGCCCACTCCCCGTCCCAGCCCTGCCCCTCTGCTCACCGCGCCCCTGCTCTCAG
Seq C2 exon
CCCGGGCCCCAGAGCTGTTTCCTGAAGGAGCCCAGAGGATGCAGCAGCTGGCACCCAAAGTGGGCCTGAACCCCAGCCAGGGCGTCCTGCTGCCCAAGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030296:ENSBTAT00000042776:4
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=0.343
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(26.2=100)
A:
NA
C2:
PF0006118=Lipocalin=PD(23.4=94.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TATGGCCCAGACCGACATCAG
R:
CTGACTTGGGCAGCAGGAC
Band lengths:
212-469
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development