BtaINT0119599 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015074 | PTGDS
Description
Bos taurus prostaglandin D2 synthase 21kDa (brain) (PTGDS), mRNA. [Source:RefSeq mRNA;Acc:NM_174791]
Coordinates
chr11:106249434-106249756:-
Coord C1 exon
chr11:106249617-106249756
Coord A exon
chr11:106249511-106249616
Coord C2 exon
chr11:106249434-106249510
Length
106 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
CCAGGATGACCTGCCCACAGGAA
3' ss Score
4.76
Exon sequences
Seq C1 exon
TTTCTGGGGCGCTGGTTCACCTCCGGCCTTGCCTCCAACTCGAGCTGGTTCCTGGAGAAGAAGAAGGTGCTGTCCATGTGCAAGTCTGTGGTGGCCCCCGCGGCGGACGGCGGCCTCAACCTCACCTCTACCTTCCTCAG
Seq A exon
GTGGGCAGCGGGGCGGGCATCTGGGGCCCAGAGCTCCCGGCGCAGGGCCGCAATCTGGGGACACGCCCAGCACCTGACCCCTGACCCCAGGATGACCTGCCCACAG
Seq C2 exon
GAAAGACCAGTGTGAGACGCGGACCTTACTGCTGCGCCCCGCCGGCCCCCCAGGCTGCTACAGCTACACCAGCCCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015074:ENSBTAT00000020065:2
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:
PF0006118=Lipocalin=PU(31.0=95.7)
A:
NA
C2:
PF0006118=Lipocalin=FE(17.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTCTGGGGCGCTGGTTCA
R:
CAGTAAGGTCCGCGTCTCACA
Band lengths:
171-277
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development