BtaALTA0016389-3/3 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000039531 | LCN12
Description
lipocalin 12 [Source:HGNC Symbol;Acc:HGNC:28733]
Coordinates
chr11:106277605-106277867:-
Coord C1 exon
chr11:106277788-106277867
Coord A exon
chr11:106277629-106277708
Coord C2 exon
chr11:106277605-106277628
Length
80 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
TGACGAGGCTGCCTCGCCAGAGC
3' ss Score
1.12
Exon sequences
Seq C1 exon
GGGCCAGCGCTGTGTCACCTGGTCATATGAGCTTATTTCGCAGTCCCAGCCTGGGACGTTCTCGGTGGATCACAGTGGAG
Seq A exon
AGCCCGGGGCGGACCCCGAGGAGATCCAAGTGTATGACACGGACTACGCGTCCTTCGCCCTCCTACTCTCCAAAAAGCAG
Seq C2 exon
TCGGACCTGCAGAGGATCCTCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000039531-6-7,6-6,6-5-3/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.214 A=NA C2=0.125
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(18.5=100)
A:
NA
C2:
PF0006118=Lipocalin=FE(26.9=100)
Other Inclusion Isoforms:
NA
Other Skipping 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:
96-176
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development