GgaINT0048640 @ galGal4
Intron Retention
Gene
ENSGALG00000012526 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr7:35054043-35054423:-
Coord C1 exon
chr7:35054332-35054423
Coord A exon
chr7:35054160-35054331
Coord C2 exon
chr7:35054043-35054159
Length
172 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
GTTTGTTTGCTTATTTACAGGAT
3' ss Score
8.85
Exon sequences
Seq C1 exon
GATCAACAGCACTTGATCTCTTCAAGTTCTATGTTGAAGACTTAAAAGCACGTTACCATGATGAGAAGAAGATCATAAAAGATATCCTAAAG
Seq A exon
GTGAGAGGGGAAGTTGCCCCGTTTTGCTGTTTTTGTCTTAATGAGAGATTTCCCTTTCTTTTGGGAGATGTGCCCTGAACACGGTGGGAAATCCCACGCAGCCTCTTAGTGAGACAATTCCTCACTCACTCCCTGGCCAAGAAAGTAAGTTTGTTTGTTTGCTTATTTACAG
Seq C2 exon
GATAAAGGATTTGTGGTTGAAGTGAATACTTCTTTTGAAGACTTTGTCACAGTCATCAGTTCAACTAAGCGAGCCACCACTTTAGATGCAGGAAATATCAAGCTGGCATTCAACAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012526:ENSGALT00000020462:17
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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAACAGCACTTGATCTCTTCA
R:
ACTGTTGAATGCCAGCTTGAT
Band lengths:
207-379
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]