BtaINT0112110 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007946 | PIPOX
Description
Bos taurus pipecolic acid oxidase (PIPOX), mRNA. [Source:RefSeq mRNA;Acc:NM_001014878]
Coordinates
chr19:20973943-20974621:+
Coord C1 exon
chr19:20973943-20974156
Coord A exon
chr19:20974157-20974438
Coord C2 exon
chr19:20974439-20974621
Length
282 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACA
5' ss Score
5.49
3' ss Seq
TCCCTGTTCTGCCCTTTCAGGAT
3' ss Score
12.64
Exon sequences
Seq C1 exon
GCAGACTGGACTACTGCTGCTGGGAATGAAGGAGAACCCAGAATTAAAGATAATCCAGGCTACTTTGTCGAGGCAGGGAGTGGAGCACCAGTGTCTTTCATCTGAGGAACTGAAGCAACGTTTCCCCAATATTCGGTTGGCCAGGGGAGAAGTGGGGCTCTTGGAGGTGTCCGGAGGAGTTCTCTATGCCGACAAGGCACTCAGAGCCCTCCAG
Seq A exon
GTGACATGGTGCATCGTTAGGGGCCACACAGCTCCTGCTCTGGGCATCCTGGGTCCCCATCAGCCATCCCCTGACCTCCGGCCGGATGAGCGCCTTTGCCCTGCTGCTTCTAGTCTTGACTATGGGGGCAGGGCGATTTTAGATATCCTATTAGGCCTGGACAATATGGGTGAGGAGGTCTAGAGTCTGCCCTCTCTTTTCTGCCCTCAGTGAAGGATTCTTTGTCCACCAGGGTGAACCACATATAAAACTGATTCTTCCTTCCCTGTTCTGCCCTTTCAG
Seq C2 exon
GATGCAATTCGACAGCTAGGTGGCATAGTGCATGATGGAGAGAAGGTAGTGGAGATAAAATCAGGGCTACCAGTCATGGTGAAAACTACCTCCAGGAGCTACCAAGCCAAGAGCTTGATCATCACGGCAGGTCCTTGGACCAACCGGCTCCTCCGTCCCTTGGGAGCTGAGCTACCTCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007946:ENSBTAT00000010444:3
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=0.000
Domain overlap (PFAM):
C1:
PF0126619=DAO=FE(19.8=100)
A:
NA
C2:
PF0126619=DAO=FE(16.8=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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCTGCTGGGAATGAAGGAG
R:
GCTTGGTAGCTCCTGGAGGTA
Band lengths:
308-590
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development