GgaINT0048629 @ galGal4
Intron Retention
Gene
ENSGALG00000012526 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr7:35060669-35061350:-
Coord C1 exon
chr7:35061240-35061350
Coord A exon
chr7:35060799-35061239
Coord C2 exon
chr7:35060669-35060798
Length
441 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACA
5' ss Score
8.1
3' ss Seq
TTTGTTTTTGTGTCCATTAGCAA
3' ss Score
5.4
Exon sequences
Seq C1 exon
AAATCGACGTGGACGGAACACAAATCACCTGATGGAAGAACCTATTACTACAACACTGAAACAAAGCAGTCCACGTGGGAGAAGCCAGATGATCTTAAAACACCTGCTGAG
Seq A exon
GTAACAGTTCAGACAGATTGCTGTGTGACTTTGTGTGAAGGCGTGGTTTACTGCCGTGACTTCCACATGGCAGAGCTGTGCCAACACATTTTTATCAATGGGAGCAAATGCCTGTAAGCATTTCTACAGCTTTTCTAATTTTATCACCTTCCTTACATTGGTGCAACTTGAAGCTGCAAACTAAACAAAATTCTAAGCATTTTTTCCTCAATTCTAAGGTCAATTTCCATTATTGAAAGGCTGGCACTTATTTAAGTGATGTGTTTGTGTCACTAGAGAGTATCGAGGGTCCACGAACGCGGTGAACACGATCCCTTGTGTTCGCTGATCCTTAAACTATCACTTGGCTTAGTAGTATTACAGGCTCACTTCTAGCAACCTTTTTAGTTTTAAAATACTACTGTAAGTTTGATTGGATGTCTTTGTTTTTGTGTCCATTAG
Seq C2 exon
CAATTGCTGTCTAAGTGCCCCTGGAAAGAGTACAAATCTGATTCTGGAAAGCCATACTACTATAATTCCCAAACAAAGGAATCACGCTGGGCAAAACCCAAAGAACTCGAAGACCTGGAAGGTAACATCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012526:ENSGALT00000020462:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.771
Domain overlap (PFAM):
C1:
PF0039721=WW=PD(93.3=75.7)
A:
NA
C2:
PF0039721=WW=WD(100=68.2)
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:
AAATCGACGTGGACGGAACAC
R:
CCTTCCAGGTCTTCGAGTTCT
Band lengths:
233-674
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]