DreINT0112201 @ danRer10
Intron Retention
Gene
ENSDARG00000017910 | pdss1
Description
prenyl (decaprenyl) diphosphate synthase, subunit 1 [Source:ZFIN;Acc:ZDB-GENE-030131-4430]
Coordinates
chr24:5985970-5987435:-
Coord C1 exon
chr24:5987355-5987435
Coord A exon
chr24:5986456-5987354
Coord C2 exon
chr24:5985970-5986455
Length
899 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
ATTTTCTGTGTCTCGCTCAGAGT
3' ss Score
8.71
Exon sequences
Seq C1 exon
TTTCCAGAGCTTCATTCCATGATCATGAGGCGCTTCAGCTCTGATGGAGATGTGGATCGAGCCTGGCAATATGTGCTGAAG
Seq A exon
GTCAGTTTTACAGTCAATATCCTCAAAACATGACCAGATCATGCCTAAAGTATGCTAGTAGATGCTTTACTTCAGATGTTTTGTAATTGTAATTGTAATTACAGTAATTCTACTGTATGATAGTTCAAAATAATCATTTAACTGCGTATCTGTGAATATTAACTGAATACTGTACTTTACTATATTATTTTATAAACATCTGCAAACATGACAATTTATTAAATTAGAAAATAGACAAGTAATTATTTAATTAAACGTAAAGCTGACAGAAATGAAAATAACTGATAGGAGTATTCACTAACTTGCACAAAATTCAGTCACAAGATAGCGCCAAACAGTCCAAAACGTAAAGCTAACAGAAATTAAAACATCTAATGGAGGTATACTCTAACCTGTGCATTATTCAGTCACAAGATGGCACCAAACAGTCAAAAAATAAAAACATCTGCTTGAAAATACACTAACCTATGCATTATTCAGTCATAAGATGGCGTATGAGCCTATGTTTTTCAGTGGTTATTATGTGGGAATAACATACCTTAGAATATAGTAATTGACCAATCAGAATTGAGTATTCCAAACAGCCGAGTAATAATCTGCGATAACAACCATCTGGACGTAATTTGTCCCTTAGTATACACTAACCTGCACATTATCACTAACCTACATATTGTTCAGTTACAAGATGGCAGTCAAAAACTAAAAACAGCTGGTGGAGTAAACACCAACCTGCACATTATTCAGTAACCAGATGGCGGTTGTTATCTGGGAATAACATTGCTTGGACTATTGCGACTGACCAGAATCGAGTATTCCAGACAGCCGTGTTAATTTCTGTTAACAACCGTCTGGATGTACATTATCCCTTACTTAGCTTGTATTTTCTGTGTCTCGCTCAG
Seq C2 exon
AGTGACGGTGTTGAACAGACGAACTACCTCGCCCAACACTACTGCCAAGAGGCCATTCGTCAGATCAGCCGGCTGCGTCCGTCCAGTGAGAGAGACGCTCTTATTCGATTGACGGAGCTGGTGCTGCGCAGAGACAAATGAGCCCGGCAGAGCTCCGCCCTCAGGCAGCTACACCTCTACACACAGAGAACATTTACACCACACTGTAAGCTTTACCGTACTGTTACGGCAGAGGATGACTGTGAATGAACGACACACTCTGCCAAGACCACCAGAATTCCAGGTGTAGCACAGACAGAGGTGCTACTGTCACTCATGTGTGTGTGTTTATGTGGATCCGTTAGAGATGCTTTAACATCCGTCCACATTACAGAAGGCCAAACGTCTCGATTTCTTGTTGATGTGCTTTTGCGTAAAGTGCTCAGTAACAGCCAAGGCCTTAAATTTCACTATTTACTCCAATTAAATAAGGTATTTTTTAAAGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000017910:ENSDART00000040865:10
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:
PF0034812=polyprenyl_synt=FE(10.0=100)
A:
NA
C2:
PF0034812=polyprenyl_synt=PD(4.2=23.4)
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:
CCATGATCATGAGGCGCTTCA
R:
TTCTGGTGGTCTTGGCAGAGT
Band lengths:
342-1241
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]