BtaINT0084908 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030296 | LCNL1
Description
lipocalin-like 1 [Source:HGNC Symbol;Acc:HGNC:34436]
Coordinates
chr11:106245809-106246501:-
Coord C1 exon
chr11:106246264-106246501
Coord A exon
chr11:106245949-106246263
Coord C2 exon
chr11:106245809-106245948
Length
315 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGC
5' ss Score
9.1
3' ss Seq
CTCGCCCCGTCCCCCTGCAGTTC
3' ss Score
10.11
Exon sequences
Seq C1 exon
ATCAGAGGGGGCATGTCCCAGGCGGGCAGGCCAGCACACCGGGGCGTCTCAGGGGCATAAAGGCACAGTGGGAGAGGCCACCCCAACCCTCCTGTCCTGCTCCTGAGCCCTGTGCCGTCGACAACAGCCACCTTCCAGGATGCTGCAGACGCTGCTGATCAGCGGGACCCTCGCCCTACTCGCTGCAGCCCCAGGCCAGGCCCAGGTCCCCATCCAGGCTGACTTTGATGCCAGCCAG
Seq A exon
GTGCGCATGGACATGCCCGGGCTGGCAGCCTCTGTCTGACTGCATTCTACCAGATAGGCCAGAGGGCTGGGGGAACCCAACCCAGCCCCCACTCTGGTTCAAGCTCAGCTCAAGGGGACCAAGCCCGCATCTGTCTGCCCAGCTGACTTGGGGCGGGGGGCTGCAGAGGAGAGTGGGCCCCTCAGCCCCTAGTCTGACTTCTGTCCCCACCACTTGCTGGGCCGCCAGCCAGATGAGTTGCAGCTGCCCCCCAAGTTCGACTCAGGTTTGATGTGGCAGCCAGGGCTGCCCCCAGCTCGCCCCGTCCCCCTGCAG
Seq C2 exon
TTCCAGGGCCCCTGGTACGTGGTTGGGGCGGTGTCGGACGACCAGAGCTTCCTGGATGCCAAGGACAACATGAAGATGCCCGTGGTCTTGGTGACCTCCTTGGCCAACGGCAACCTGGGCATCAAGTTTGGGTTCCCCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030296:ENSBTAT00000042776:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0006118=Lipocalin=PU(31.9=95.7)
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
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:
ATCAGAGGGGGCATGTCC
R:
GCCAAGGAGGTCACCAAGAC
Band lengths:
342-657
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development