DreINT0112200 @ danRer10
Intron Retention
Gene
ENSDARG00000017910 | pdss1
Description
prenyl (decaprenyl) diphosphate synthase, subunit 1 [Source:ZFIN;Acc:ZDB-GENE-030131-4430]
Coordinates
chr24:5994169-5995137:-
Coord C1 exon
chr24:5994953-5995137
Coord A exon
chr24:5994225-5994952
Coord C2 exon
chr24:5994169-5994224
Length
728 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCG
5' ss Score
9.18
3' ss Seq
TTTTTTTGTTTGTGTTTCAGGTT
3' ss Score
12.83
Exon sequences
Seq C1 exon
CTGACGTCACTGGGCATGTGCGGCTCTCGGTTGTGTGTGCGAGCATGGCGGTGCCGTGGAGCCGATGCTGGAGGAGCAGCACAGGAGCTGCTGTATTACTACAATATTGTTGTATTTCCAGCAGAAGAGCTTTCACTCCAGCGGCTTCAGCAGGAAGAAAAGCTGCTACTTCCGCCGCCACACAG
Seq A exon
GTATCGATCACACTGAAGCACACACGGATGATGAAGGTCACCGGTGTGCAAATGAATGACAGATCACTGCTGTGTTTGTATGGGTCAGGTTTAAGACTCTTTACAGCATATCGTGCGCTAAAACAGAGTTAAAAGCGTTCAGTTAGATGATTGCAGTCGCGTTTGTAAAGCCAACATGAGTGTTTCATGAAGTGTTCATGTTAAAGGTCAGGAGTGTGCGGGAGTAGAGACACTTCCGCTGATTTGTAGTTTACTGAAACTCACTGAAGAAGAAGAATGTTGCTCAAGAAGACTTGACTTAAAGCATGTGTACATATATGGAGGTAAATGGCCAGATTAAGGTAAAGTTGATCTTATGTTCGGATATGTGTTCATCTTAACAGTTCTTTCCTATATAGTTTACTGCGATCATTTAAATATTTATATGTCTGAAATATAAAGTCTGACTTCAAAACAGCATTAACTTATAGCACTATTTATTTGACTGTGAACATTGTTGTACTTTGAAGGTAATTTACTGATAATACAGTTTTGTTTTTTTTTCGTTTTTGAACAATTAAACAGGACACTCTGGAACCCTTATGAAAAGAGTCTACATATTCTGATGCTGAAAACATATTTGTATTTTGACCGTGATACTCTCTGTCCTAATTACATTATTGTTTTAATGCAAACTGCATTATTCAGCCTGTATGATCTGTTTTTTTTTTTTTTTGTTTGTGTTTCAG
Seq C2 exon
GTTTTATTTCAGCAGGGTCATGTACATAGTTTTAACAAACCAGTGACTCTTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000017910:ENSDART00000040865:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGACGTCACTGGGCATGTG
R:
CTTGAAAGAGTCACTGGTTTGTT
Band lengths:
241-969
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]