GgaINT0111784 @ galGal4
Intron Retention
Gene
ENSGALG00000009743 | RPAP3
Description
RNA polymerase II-associated protein 3 [Source:RefSeq peptide;Acc:NP_001006231]
Coordinates
chr1:31382517-31383418:-
Coord C1 exon
chr1:31383260-31383418
Coord A exon
chr1:31382658-31383259
Coord C2 exon
chr1:31382517-31382657
Length
602 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
AAGTACTTATTTCAATATAGAAT
3' ss Score
3.21
Exon sequences
Seq C1 exon
ATTACAATGACTGCATCAAATAAAGCACTGGAGCTTCAGCTGCAGATGAAGCAAAACGCTGAGGAACTGCAGGATTTTATGAGGGAATTAGAGAGCTGGGAAAAGGATATTAAAGAAGTTGATTCAGAATTAAGGAAACAGAGTGGTGTCTCAGAAGAG
Seq A exon
GTAAAATCAGTGGACTTGTGACTATTATTATTTATTTTAAGATACGTCAGTGTTTGTAATCGTGCTATAAAAGCATACTTGTTTTGCAGATGTTATATTTCAGAGAACACAGTTAACTTCATCAAATTATGTTCTGATTTAAAATACCTGAATAGATGGTAAGAGCTGATTTGTTCTTCATCTAAAGTAGATCCCACTGCAAATTGTTCTGCTAACACAGCTGTGAATCCATAGCCTGGAGGTCATGAATGCTTGGGGCTGATAAATGTTTGATCAGTTCCTGATAGATCTAGTAGAATATTTCTGTCAGTAGCATCAATATTACTTATTTATTGTGCACTCTTAATGTATTAATCAGTGATACTCTGCAGAAAGTTGTCTTCTAAAACTTAGCATTATATCTATATAATACTATATATTGAAAGATTTATACTCACTATCCTTTTTTGTAGAATTCCTGACAACAGCTTTCTTGATGGATTTATGAAATAAAACTAGACTGTAGATGGAGATACCTATGTGTAGACATAGGTACTAAAGATTATTCAGTACAAGCAACTTTTGTATGTCTGTTTTATAATAAAGTACTTATTTCAATATAG
Seq C2 exon
AATTTACCACCCATTCGAAACAAGACTTTTAAGAAAAAGAAGAAAAGCAAGACTAAAGTCCCATCAAAGACAACCACTGAGGAAAACAAGAAAAACAAGATCAAGTCTTATGATTATGAAGCTTGGGGAAAACTTGATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009743:ENSGALT00000015853:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.675 A=NA C2=0.660
Domain overlap (PFAM):
C1:
PF138631=DUF4200=PU(92.5=96.1),PF075448=Med9=PU(96.0=94.1)
A:
NA
C2:
NO
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:
ATGACTGCATCAAATAAAGCACTGG
R:
CACATCAAGTTTTCCCCAAGCT
Band lengths:
294-896
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]