GgaINT0048638 @ galGal4
Intron Retention
Gene
ENSGALG00000012526 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr7:35054584-35054938:-
Coord C1 exon
chr7:35054805-35054938
Coord A exon
chr7:35054699-35054804
Coord C2 exon
chr7:35054584-35054698
Length
106 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGGT
5' ss Score
8.08
3' ss Seq
GTAGTTTATGTATTTTATAGATA
3' ss Score
5.97
Exon sequences
Seq C1 exon
ATATGGATAAGGAGGATGCACTGATCTGCTTTGAGGAACACATCAGGGCACTGGAAAAAGAGGAGGAGGAAGAAAAACAGAAAAGTTTACTGAGAGAAAGAAGGCGGCAGCGGAAAAACAGAGAATCTTTTCAG
Seq A exon
GTTGGTGGACTTGCTGTTTGTCCTAGGCATGTCAACTGATTACATACATAGTCTGTGCTCCCTGTTTCTTGGGGATAAGCTAATGAGTAGTTTATGTATTTTATAG
Seq C2 exon
ATATTTTTAGATGAACTGCACGAGCACGGACAGTTACATTCGATGTCCTCTTGGATGGAGTTGTACCCAACCATAAGCTCTGACATCAGATTCACTAATATGCTTGGTCAGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012526:ENSGALT00000020462:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.200 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0184614=FF=PD(23.2=28.9),PF0184614=FF=PU(10.7=13.3)
A:
NA
C2:
PF0184614=FF=FE(67.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGATAAGGAGGATGCACTGA
R:
CTGACCAAGCATATTAGTGAATCTGA
Band lengths:
242-348
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]