GgaINT0048642 @ galGal4
Intron Retention
Gene
ENSGALG00000012526 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr7:35053029-35053794:-
Coord C1 exon
chr7:35053657-35053794
Coord A exon
chr7:35053125-35053656
Coord C2 exon
chr7:35053029-35053124
Length
532 bp
Sequences
Splice sites
5' ss Seq
GATGTATGT
5' ss Score
6.31
3' ss Seq
CATTGCTGTTTCTCTGGCAGATC
3' ss Score
11.07
Exon sequences
Seq C1 exon
CTGCTGGAAAAGGCAGAAGCCCGTGAAAGAGAAAGGGAAAAAGAAGAAGCTCGCAAAATGAAGCGGAAAGAGTCTGCCTTCAAGAGTATGCTGAAACAAGCTACTCCTCCCATCGAGCTGGATGCTGTCTGGGAAGAT
Seq A exon
GTATGTATTGCTGCTTCATTATGGAAGTCATTCCATATATATTCAGCAGGTTGATACATGCTAATAACTAAGCCTGCATTCTCTGTGGTCGTGGTTTCTGCTTATACAGACCCGTAAGAATGAGTCACCTCTTCAGCAGACATCAGAATTGGAGTTGAAAATTTTAATTCTATCAATACCTCCATTTGGTTTATTTTAAGCGAATGGTTTAAGAGGAGATTAAAGGACTCTGCTCAGTTGAAAGTCTAACTTTGTTCTGGTAGGATTAAAGCCTTTTCTGTCACAGCGTACTTCACGGTACGCAGTGTGCTTTTACTGAGCTTGTGAGGCATATGCAGAAAAAAAACAATTCTGCATGCACGTGTATCCATTTGTGCAGTTGTAATAAAGACCCTGCTGGTTATAGAGCTGACAAGAAACAATCCGAGCCTGTAACAGCACCGTGGCTTTCCCAACTGGTGGAGTAATGTCATCTGTAAGCTTCAGAATGTCTGCATTTCGTGTCAGTATTTCATTGCTGTTTCTCTGGCAG
Seq C2 exon
ATCAGAGATAGATTTGTGAAGGAACCAGCATTTGAAGACATCACTCTGGAGTCTGAAAGGAAAAGAATATTTAAAGATTTCATGCATGTACTTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012526:ENSGALT00000020462:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.473 A=NA C2=0.156
Domain overlap (PFAM):
C1:
PF0184614=FF=PU(46.2=52.2)
A:
NA
C2:
PF0184614=FF=PD(50.0=81.2)
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:
TGCTGGAAAAGGCAGAAGC
R:
TATTCTTTTCCTTTCAGACTCCAGA
Band lengths:
206-738
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]