BtaINT0084890 @ bosTau6
Intron Retention
Gene
ENSBTAG00000039531 | LCN12
Description
lipocalin 12 [Source:HGNC Symbol;Acc:HGNC:28733]
Coordinates
chr11:106279085-106279698:-
Coord C1 exon
chr11:106279582-106279698
Coord A exon
chr11:106279222-106279581
Coord C2 exon
chr11:106279085-106279221
Length
360 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGG
5' ss Score
6.23
3' ss Seq
CTACCCCCGGCCCCCTGCAGTTC
3' ss Score
6.65
Exon sequences
Seq C1 exon
ATGGGCCCATGGTTGGCCCTGTGGGTGCTTCTCTACCTGCCGAGAGCCCTCCAGGGCCAGAGCCCACACACCCGGGCGGCCCCCAGCTCTGTTCTGCAGAGTTTCGAGGACAGCAAG
Seq A exon
GTCAGGGCCAAGGAGGGATGGGAGGTGCCCGCCAGGCCTGGGTGTGGGGAGTCAGCCAGGCCAGGTCTCTGGGCACCCCCACCATGGAGACCCCTGGCCTCTGGCAGCAGAGAACCCTAGACTCCCCTGTAGTCCCCACCTCTCCCTGTGGAGTTGGGGGGAATATCTCAGTCCCTCTGCCCAGAGAGCCCCCCCGGCCAGCATACAGTCCCTGTGGGGCCCCCCCAGCCAGCGTCACAGTCCCTGCGAGGCCCGGGCTCTCTCGGGCTCCTGCCAGCGTGACCGAACACCGGGAGCTGTTGCCGAGTGCAGCAGGGTTCCCGGCCAGCCCGGCCCCTGCCTACCCCCGGCCCCCTGCAG
Seq C2 exon
TTCCAGGGGGAGTGGTATGTCCTCGGCCTGGCGGGCAACACCCACACGGTAGCAGACAGGTCCCTGCTGAGCCCTTTCACGGCGACGTTCGTGCTAAATAAAAACAACCACTTGGAAGCGGCATACGCCATGATCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000039531:ENSBTAT00000032576:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.077 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0006118=Lipocalin=PU(30.1=95.7)
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:
CCATGGTTGGCCCTGTGG
R:
CGTATGCCGCTTCCAAGTG
Band lengths:
238-598
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development