DreINT0120525 @ 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
chr9:4740833-4741126:+
Coord C1 exon
chr9:4740833-4740924
Coord A exon
chr9:4740925-4741009
Coord C2 exon
chr9:4741010-4741126
Length
85 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
GCTTGTGTGTTTTGTTCCAGGAT
3' ss Score
10.48
Exon sequences
Seq C1 exon
GCTCCACGCCTCTGGACTTATTTAAGTTTTATGTGGAGGATCTGAAAGCTCGTTACCATGATGAGAAGAGAATCATTAAAGACATCCTGAAG
Seq A exon
GTGAGTGTGAGACTGCGGTGATCAGTGTTTATCAATTTTTGCGCTGAATCATTGGTGAAATGTGTGCTTGTGTGTTTTGTTCCAG
Seq C2 exon
GATAAAGGTTTCCTGGTGGAGATCAACACAGGCTTTGAGGACTTTGGCTCAGTGATCAGCTCTGATAAACGCGCCACCACGCTTGATGCGGGAAACATCAAACTGGCCTTCAACAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058467:ENSDART00000081326:18
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:
PF0184614=FF=PD(17.9=32.3)
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:
TGTGGAGGATCTGAAAGCTCG
R:
AGGCCAGTTTGATGTTTCCCG
Band lengths:
170-255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]