GgaINT0048639 @ galGal4
Intron Retention
Gene
ENSGALG00000012526 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr7:35054332-35054698:-
Coord C1 exon
chr7:35054584-35054698
Coord A exon
chr7:35054424-35054583
Coord C2 exon
chr7:35054332-35054423
Length
160 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TTATCTAGTTTCTTCATCAGGAT
3' ss Score
5.54
Exon sequences
Seq C1 exon
ATATTTTTAGATGAACTGCACGAGCACGGACAGTTACATTCGATGTCCTCTTGGATGGAGTTGTACCCAACCATAAGCTCTGACATCAGATTCACTAATATGCTTGGTCAGCCTG
Seq A exon
GTAAGAATACTTCCAACCCTGTAAAAAGTAGACGTAAAGCTCTCAGATGTTGGCAGTCTGAAGCAGGGTTGTCTGAATGTTGTTCTAAAATGAAAAATAATTAAAAAAACGCAGCTCTTTTATTAGAGCTAGCTTTTGACTTATCTAGTTTCTTCATCAG
Seq C2 exon
GATCAACAGCACTTGATCTCTTCAAGTTCTATGTTGAAGACTTAAAAGCACGTTACCATGATGAGAAGAAGATCATAAAAGATATCCTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012526:ENSGALT00000020462:16
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=FE(67.9=100)
A:
NA
C2:
PF0184614=FF=PD(17.9=32.3)
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:
TTTTTAGATGAACTGCACGAGC
R:
TGATCTTCTTCTCATCATGGTAACGT
Band lengths:
187-347
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]