BtaINT0112114 @ bosTau6
Intron Retention
Gene
ENSBTAG00000007946 | PIPOX
Description
Bos taurus pipecolic acid oxidase (PIPOX), mRNA. [Source:RefSeq mRNA;Acc:NM_001014878]
Coordinates
chr19:20976460-20978420:+
Coord C1 exon
chr19:20976460-20976535
Coord A exon
chr19:20976536-20976828
Coord C2 exon
chr19:20976829-20978420
Length
293 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
ACCTGTTCTCCTTTCCCTAGGGC
3' ss Score
13.06
Exon sequences
Seq C1 exon
AACACCCCCGATGGGCACTTCGTTCTTGATAGACACCCAAAGTACGACAACATTGTCATTGGTGCTGGATTCTCTG
Seq A exon
GTGAGCCTGAGCGAGGGAAGATGGGGTGCCTTAAAGCTGACCTCGGTGCAAGACAGAATGGTGTTTTTCATGCTTTAAGCTGATAGAGGAGGGCCAAAGTCCAGATTGTGCGTGTATAAGGGGGCTGAACGGGGCTATCAGAGAATAAGGGGTGCTCATGGTGGGAGGCAACTTCTGCCTTTGGGGTGCGACCGGTGGGAAGGTTAACCCTGTCTGGGGACTGTGTAGGGGACTTCCAGGGAGCCCAGCCCCTGTCTATGAGGATGCCTGACCACCTGTTCTCCTTTCCCTAG
Seq C2 exon
GGCATGGGTTCAAGTTGTCCCCTGTCGTGGGGAAGATCCTGTACGAATTAAGCATGAAATTAACGCCATCCTATGACTTGACACCTTTTCGAATCAGCCGCTTTCCCAGCCTGGGCAAAGCCCACCTTTGACCCCCTGGCCAGCAGCTCCCCTTCTGTGCCCAGGAGTTGGAAATAAAGCTGGGAAAGACATGTAAGAGGAAGAAAAAGGCTGTGGGAGGCTATCCTTTCCTCGTGACTCTCTTCAGTCCCCCATAAACACCGGCTGATTGAACGTACCTTCTTTCTCTGGCCAACTCCCCAATCACACACCACTTTTTTGCTTCAGTTCAATCAGATATTCTACAATCACAGAGTGCCAAGGACCTTGGAGGTGGATGTCTCAGTAAGGAAGGGGCATAAGGACCGGCTCAGGAGACCAAAACAGCTATTAAAATTCTCTTCACGGGGGCATTTGTTGAATTTTGGATAGATCTGATGAAAGTTGCCTAGGGGAGGGTAAACAAGATAGTCTGTAGACCATTCATGCCCGTGGAGCTCCTTTTCATAAAACTAGAGCCATCCTCTATCACGAACCCCCACAAAATGTGGCTCGTCGTGGGTGCACAGCAAATGTTTGTTGAAAAAAAAAAAAGTGTTGAACAAACAGATAAGTAAATGACTGCCTTGCATGAAAGCCTGTGGCGGGCTTTATTTTCCATGTGACCTTATTTCTTACAGAATTTAATTGTCTGAATTAGCACCACAGAATCCATTACCCCAGGACTCCTTAGGGTCTTTATCCCCTCAACGCACCACACCCTCTTTCTCTGGATTCTTTGTCTGGCTCTCTCCTCTCATAAAGACGCTCGGCTCCCCAGTCTCTCATTAAGGTGTATTGTCAGGTCTTTATGAAGATGGAGCTGTTCTACCAGAAAGGAAGAGAGAGACACACTCGCTCAGAAACCCTGTTCAATGTTTGAATGTTAAATGTGCCATTTTATTATCATTAGGATTGCTCCCACTTAATGAAACAGCATTAACACCGAGTCGGCTGGCCTCCTTGCACTAATTGCTTTGGAAGGAAACAGGCTCATAACTGCCCCAGGGTGGGCGGAGGGGTGAGAGGTGTAAACAGAGACTCAAGCAAGGCTGAGCGCATTCAGATGAAACCCAAGCAGGAGCATCTCCAGACAGGGGCCCCTTGGACCCAAAAGAATAGGAGTTAATGAGCTCTGGGGAGAAAAAAAAAAAAAAAAAAACTGGGACTGGGTGGGCTGGAAATGTTTAGAGGAATCCCTGAGGGGGGAGGAGTGGGAAATGAGAAAAAGAGTAAAAATATTCTCAAAGGAAAAACAACACAGAGGAAATTAGTCTTCAATTGCCGCATAGGCCTAGGCACATGGATTAATGCTGATTTCTCCTGGGAATTATAAAAGCTAGCCAGTTGGAATGAAACATCATTCCAACTCTGCATTTTGGGTGCTCTCATTTGGTTCCCTGAGCCACAGCCTCTGTAAAGGGGCGGGGGAGGATAATCATATCTGTAAAATGGGAATATTAAATCTCATGGATCAATCTTGAAGACATAATGCTGAATAAAATCATCCAGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000007946:ENSBTAT00000010444:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0126619=DAO=FE(7.0=100)
A:
NA
C2:
PF0126619=DAO=PD(4.5=36.4)
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:
CGATGGGCACTTCGTTCTTGA
R:
CGAGGAAAGGATAGCCTCCCA
Band lengths:
302-595
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development