BtaINT0109712 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006529 | PDSS1
Description
Bos taurus prenyl (decaprenyl) diphosphate synthase, subunit 1 (PDSS1), mRNA. [Source:RefSeq mRNA;Acc:NM_001100331]
Coordinates
chr13:18200342-18202102:-
Coord C1 exon
chr13:18201961-18202102
Coord A exon
chr13:18200454-18201960
Coord C2 exon
chr13:18200342-18200453
Length
1507 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGT
5' ss Score
10.75
3' ss Seq
AGGTTTTTCTTCTTTTCTAGGCT
3' ss Score
10.05
Exon sequences
Seq C1 exon
AAATGTGCAAGCAAGCCAGCGTGCCATTGCCTTAATTGCAGAAATGATCCATACTGCCAGTCTGGTGCATGACGATATCATTGATGATGCAAGTTCTCGGAGAGGAAAACACACCGTTAATAAGATCTGGGGTGAAAAGAAG
Seq A exon
GTACGTGCAGCTTTTTGGGTTTTTTCATCTTTCATATTAAATGCCACACTCTTTGGATTGCATTTATTTTTCAGATTTGTCTCAAATGATGAAAATGTGTTTCATCAAATGTGGTCTTCTAGCTTTCAAAATAGTTTCTTGTATATAGCTTTCATCTATATACAGATGTTTGATTGTAGATAATACCATAGAAAAATAAACTTACTATTTCTATTTAATCACAGTTTTACATAGAATTCGGTTAAGGAAAGCATATTTGTAGTTATCCAAAAAGTGTCTCTTATGAGGAGTCACACCTTTTACTCGGGGTGGAGGTGGATGTTGTGAGCCTGTAAGTCACGATGTGTACAGTGACTTTATCAGTGTGCATTTACAGTTATGTCAGGGTACCTCATACAGTGTATGTTGTATAAAATGATGTTTAGTTGGTAAACAAACTGAACATCACTAATTTTTAAATGCCGGAGAACTAATAGACAATAAAAACTTGGAACTTCTCTGGTGGTCCAGCAGTTAAGACTCCACGCTTCCACTGCAGGGGGCATGGGTTCAATCCCTAGTTGAGGAACTTAGGTCCCACGTGCTGTGTGGAATAAAGACTGAAAATGTGGTTATGTTGCATATTCTAGGGATTAAAATTTCCATGAACTCTATCATTTATAACTACTCTTTAACACTTATGCATATCCTTTAAGTATGCAAATTAGTATACTTGATTATTGCATATAATCCAATCATATGGTTTATAATTAATGGCAAACAGTGCAAACATTTAACTCATCATCTAAAGAAGATTGAAAAAGTATCCATGCATGTTCAGTGAAAAAATGTCTTGTTCTGGAATGATAGGCCGTGTAATAGTGTACTAAGAGCTTTGAACTTGGAGCCAGGGTTCCTTGGTTTAGGTTTCATTGAGCAAAGCACGCGTGGGGCCATGGTGTGTGCCAAGTACTAGCTGGGTGATTCACAATCTGTGCCCTTAGGGGTTTGGCAAATAGGAAAAAAGTGGGAAGAGAGCAGTGCCCGAGGGGCGCTGTGCTCACAGGTCAGACCGAGGGGTCTCAGTGGACCTCCTGCAGGTACCGCCTGAGCTAACCCTGCACACGAGGCACCAGGTGAAGGGGAGGGGCTTTTTGAGCAGAAGAAACAGTAAGTGCAGAGGTGTAGCCACACGGTGTGATGGGAGAACGAATGGTCCAGAACTAAATGAAGGCAGTGGGATGCATTTTGTGGTGGCCAAGGATGAAGCCAGGGCGTCAGGCACTTCCCATCTCCAGGCGTTCGTTTCTTCAGCTCTCAACTGGAGAGACAGACTGGGTAATCTCTGAGAGCCAAGAGATTTCAAACAGGGTCCCAAACGTGTAAAATAATCCCGCTGAGGAAGAGGAAAAACGGAGACCCAGGATGAGCCCTCTCTCCCTCCCATTCTGGACTTCTCTCCTGAGAAACTTCATTGTTGGCTCCAGTGCTCGGACACTTTTCTCTGAAGGTTTTTCTTCTTTTCTAG
Seq C2 exon
GCTGTCCTTGCTGGTGACTTAATTCTTTCTGCAGCATCAATAGCTCTGGCACGAATTGGAAATACAACTGTTATATCTATTTTAACCCAAGTGATTGAAGATTTGGTGCGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006529:ENSBTAT00000008576:5
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=0.000
Domain overlap (PFAM):
C1:
PF0034812=polyprenyl_synt=FE(17.9=100)
A:
NA
C2:
PF0034812=polyprenyl_synt=FE(14.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAATGTGCAAGCAAGCCAGC
R:
CACGCACCAAATCTTCAATCACT
Band lengths:
254-1761
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development