DreINT0120539 @ 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
chr9:4726263-4726498:+
Coord C1 exon
chr9:4726263-4726383
Coord A exon
chr9:4726384-4726473
Coord C2 exon
chr9:4726474-4726498
Length
90 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
TTTCTCCTTCTTTTCTTCAGCGA
3' ss Score
10.22
Exon sequences
Seq C1 exon
CAAATGTTGTCAAAATGCCCATGGAAAGAGTATAAGTCAGACACCGGAAAGCCCTATTACTATAACTCCCAGACCAAAGAGTCTCGCTGGACTAAACCCAAAGAACTGGAGGACCTGGAAG
Seq A exon
GTCAGTAGGCAAAATGAATATAATGTTGTTGTCGTCTCTCAAATTAAGAATTGAAAATTGTTTATCTTTTTTTCTCCTTCTTTTCTTCAG
Seq C2 exon
CGATGATAAAGGCAGAGGAAAATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058467:ENSDART00000081326:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.829 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0039721=WW=WD(100=73.2)
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:
ATGTTGTCAAAATGCCCATGGA
R:
CCATTTTCCTCTGCCTTTATCATCG
Band lengths:
143-233
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]