BtaINT0084901 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017005 | LCN8
Description
lipocalin 8 [Source:HGNC Symbol;Acc:HGNC:27038]
Coordinates
chr11:106391396-106391859:-
Coord C1 exon
chr11:106391789-106391859
Coord A exon
chr11:106391501-106391788
Coord C2 exon
chr11:106391396-106391500
Length
288 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
CCTCCCGCTTGTCCACGCAGGCC
3' ss Score
10.16
Exon sequences
Seq C1 exon
CTCAGGAAGTTGTCAGACCGAAGAAATAGTGAGCTCAGAAATGAATGTTTGGGGGAAATTTGTGTTTCCTG
Seq A exon
GTAAGAGCTGCTTCCTCGGGCCCCACCCGCCAGCTCCTCTTAGCCTGGCTGCTCTTCATGCTGTTCCCTGCGCTCCTCCTCACGCCCCAGGCTCCTGTGCTCCCCACAGTGGACCGGTCATCTTGCCAGGGCTGCTCTAGTCCCCCCGAGAGGGTCCCGGCATCCCGAGAGGGTCCTGGCTAGGTGGGGGAGAATGGAGTCAGGCCCTGGCGACCCTGACCGCCCAGGCCGACCCACCCCGAGGGGTGCCCGTCCACCCAGGCCTGGCCCTCCCGCTTGTCCACGCAG
Seq C2 exon
GCCGCCGGGAGATCCACGTGGTGGACACGGACTATGAGCAGTACGCCATCCTCCGCGTGTCCCTCCAGTGGCAGAACCATGAGTTTTACGTGTTCAAGTATTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017005:ENSBTAT00000022613:3
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:
PF0006118=Lipocalin=FE(19.2=100)
A:
NA
C2:
PF0006118=Lipocalin=FE(28.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGGAAGTTGTCAGACCGA
R:
ATACTTGAACACGTAAAACTCATGGT
Band lengths:
172-460
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development