GgaINT0111784 @ galGal3
Intron Retention
Gene
ENSGALG00000009743 | RPAP3
Description
NA
Coordinates
chr1:33235935-33236836:-
Coord C1 exon
chr1:33236678-33236836
Coord A exon
chr1:33236076-33236677
Coord C2 exon
chr1:33235935-33236075
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=0.804 A=NA C2=0.660
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
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]