BtaINT0112112 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007946 | PIPOX
Description
Bos taurus pipecolic acid oxidase (PIPOX), mRNA. [Source:RefSeq mRNA;Acc:NM_001014878]
Coordinates
chr19:20975174-20975872:+
Coord C1 exon
chr19:20975174-20975326
Coord A exon
chr19:20975327-20975713
Coord C2 exon
chr19:20975714-20975872
Length
387 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CCGCTTTGATTGGGAGCCAGGTC
3' ss Score
-0.7
Exon sequences
Seq C1 exon
ACCCTGCGGATCAACGTGTGTTACTGGCAAGAGAAGGTTCCTGGAAGCTACAGTGTGTCCCAGGCCTTTCCGTGTTTCATGGGCCTGGGCCTCAGCCTGGCTCCTCACCACATCTACGGGCTGCCCTCCAGAGAGTACCCAGGGCTGATGAAG
Seq A exon
GTGAGGGGAGAGGCCCAGAGAAGGCTAACAGGGTCCCATGCAGATTTGGGGCGGCTACCCTAACTTCCCTCTCAATGAGCTCCCTCAGACCCCAGTGAGCAGCAGCAGGAACCAACTTCACCATTCAGTATGTGCCGCACGAGACTCCCAGCTGTCCTGGGGCCCAGCAAAAGGAGCCCTTCCTTTGCAAACAGAGGGTTAGCAGGGGAACGGAGGGCTAGGCAACCTTGTATGGCAACAAAAAGCATCTGACAGGAGTGCGGAAGGCTGGGGTGATGGCTGGGGTGCCTCCGGTGTACAACCTGGCCCCCCCATCTCCTGCCGGGCTGGGGGTGGTGTGCAGGAAGCCGGGGCCTCCCAGCTCAAACCGCTTTGATTGGGAGCCAG
Seq C2 exon
GTCTGCTATCACCACGGCAACAATGCAGATCCCGAGGAGCGGGACTGCCCAGCAGCTTTCTCAGACATCCAAGATGTCCACATCCTGAGCGGTTTTGTCAGAGATCACTTACCTGACCTGCAGCCCGAGCCTGCTGTGATGGAGCATTGCATGTACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007946:ENSBTAT00000010444:5
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=0.038
Domain overlap (PFAM):
C1:
PF0126619=DAO=FE(14.0=100)
A:
NA
C2:
PF0126619=DAO=FE(14.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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:
CCTGCGGATCAACGTGTGTTA
R:
CGTGTACATGCAATGCTCCAT
Band lengths:
310-697
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development