GgaINT0048636 @ galGal4
Intron Retention
Gene
ENSGALG00000012526 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr7:35055754-35056210:-
Coord C1 exon
chr7:35056102-35056210
Coord A exon
chr7:35055905-35056101
Coord C2 exon
chr7:35055754-35055904
Length
197 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACT
5' ss Score
9.01
3' ss Seq
TTATTGCATTTTCTCCTCAGGAA
3' ss Score
9.47
Exon sequences
Seq C1 exon
AAAAGCTGAACAAATGTTTGGGGAGATGGAAGTCTGGAATGCAATCTCTGAGCGTGATCGCCTGGAAATTTATGAAGATGTCTTGTTTTTTCTCTCTAAGAAAGAGAAG
Seq A exon
GTAACTTTCTTTCAGAGTTGTTCTTTTGACTTGCAAGTAAACTGCTCAATACCACTGAGTACAGAAATCTTGCAAGCAGTGCAGTTCTGTGCATTGCTCAGAGACAGCTGAAATGCAGGCAGTGGGGGAGCAATTTGTAGGATAGGCATTTGAGAAGCAGGTGAGAGCATTGCTGCATTATTGCATTTTCTCCTCAG
Seq C2 exon
GAACAAGCCAAACAGTTACGAAAGAGGAACTGGGAAGCTCTGAAGAACATCCTCGATAACATGGCTAACGTCACTTACTGCACTACTTGGTCAGAGGCTCAGCAGTATCTGATGGACAACCCTACGTTTGCAGAAGATGAGGAACTTCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012526:ENSGALT00000020462:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.176
Domain overlap (PFAM):
C1:
PF0184614=FF=PD(54.0=73.0)
A:
NA
C2:
PF0184614=FF=PU(75.0=82.4)
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:
AAAGCTGAACAAATGTTTGGGGA
R:
TCTGCAAACGTAGGGTTGTCC
Band lengths:
242-439
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]