DreINT0120531 @ danRer10
Intron Retention
Gene
ENSDARG00000058467 | prpf40a
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:ZFIN;Acc:ZDB-GENE-030131-274]
Coordinates
chr9:4747883-4748115:+
Coord C1 exon
chr9:4747883-4747976
Coord A exon
chr9:4747977-4748053
Coord C2 exon
chr9:4748054-4748115
Length
77 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGT
5' ss Score
8.94
3' ss Seq
TGGGGTATTGATCTTTACAGAGA
3' ss Score
5.05
Exon sequences
Seq C1 exon
GGCTCGGAGTCAGAGGAAGATGAGTATCACACGAAGAAGAAGAAACGTTCAACATCTAAATCTCCATCTGAGCACTCGTCCTCTGGGGAGTCAG
Seq A exon
GTCAGTGTCATTTCTCCTTGACATCTATAATCAAGACATGATGAGCATTTGACAGCATGGGGTATTGATCTTTACAG
Seq C2 exon
AGAGAAGTTATAAGAAATCGAAGAAACACAAGAAGAAGGGAAAGAAAAGACGACATAAGTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058467:ENSDART00000081326:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTCGGAGTCAGAGGAAGAT
R:
ACTTATGTCGTCTTTTCTTTCCCT
Band lengths:
154-231
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]