BtaINT0084892 @ bosTau6
Intron Retention
Gene
ENSBTAG00000039531 | LCN12
Description
lipocalin 12 [Source:HGNC Symbol;Acc:HGNC:28733]
Coordinates
chr11:106277592-106277867:-
Coord C1 exon
chr11:106277788-106277867
Coord A exon
chr11:106277712-106277787
Coord C2 exon
chr11:106277592-106277711
Length
76 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
GCCTGACGAGGCTGCCTCGCCAG
3' ss Score
-22.06
Exon sequences
Seq C1 exon
GGGCCAGCGCTGTGTCACCTGGTCATATGAGCTTATTTCGCAGTCCCAGCCTGGGACGTTCTCGGTGGATCACAGTGGAG
Seq A exon
GTGAGGGGGCGGGGGGCGGGGGGAGGAGGGGGCAGCCTGTGGGCGCTGGCGGGGAGGCCTGACGAGGCTGCCTCGC
Seq C2 exon
CAGAGCCCGGGGCGGACCCCGAGGAGATCCAAGTGTATGACACGGACTACGCGTCCTTCGCCCTCCTACTCTCCAAAAAGCAGTCGGACCTGCAGAGGATCCTCAGGGTCAGCCTGCTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000039531:ENSBTAT00000032576:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.214 A=NA C2=0.104
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(18.5=100)
A:
NA
C2:
PF0006118=Lipocalin=FE(27.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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:
CGCTGTGTCACCTGGTCATAT
R:
CTGAGGATCCTCTGCAGGTCC
Band lengths:
179-255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development