GgaINT0048641 @ galGal4
Intron Retention
Gene
ENSGALG00000012526 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr7:35053657-35054159:-
Coord C1 exon
chr7:35054043-35054159
Coord A exon
chr7:35053795-35054042
Coord C2 exon
chr7:35053657-35053794
Length
248 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
ACAATGGCCATGTGATGCAGCTG
3' ss Score
2.85
Exon sequences
Seq C1 exon
GATAAAGGATTTGTGGTTGAAGTGAATACTTCTTTTGAAGACTTTGTCACAGTCATCAGTTCAACTAAGCGAGCCACCACTTTAGATGCAGGAAATATCAAGCTGGCATTCAACAGT
Seq A exon
GTAAGTATTGATACATAGAGATACAATATGAAATCCCTGCAGACCAAAAACTAGCTCGTGTTCCCCGTACCATTACAACTGTTTCTACTTGAGAAATGCTGTTGTGTGCTTTGAAGTATTGGGCAGTGATAAATAGAAAACACCAAAGATGAACTGTCGTTGGGCTTTCCAAAAATTGCATGAAACTGAACTATTAATCTTCTGTTTTAATATTCTTCAAATGATCTCACAATGGCCATGTGATGCAG
Seq C2 exon
CTGCTGGAAAAGGCAGAAGCCCGTGAAAGAGAAAGGGAAAAAGAAGAAGCTCGCAAAATGAAGCGGAAAGAGTCTGCCTTCAAGAGTATGCTGAAACAAGCTACTCCTCCCATCGAGCTGGATGCTGTCTGGGAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012526:ENSGALT00000020462:18
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=0.473
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0184614=FF=PU(46.2=52.2)
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:
AAAGGATTTGTGGTTGAAGTGAA
R:
ATCTTCCCAGACAGCATCCAG
Band lengths:
252-500
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]