GgaINT0111783 @ galGal4
Intron Retention
Gene
ENSGALG00000009743 | RPAP3
Description
RNA polymerase II-associated protein 3 [Source:RefSeq peptide;Acc:NP_001006231]
Coordinates
chr1:31383260-31384325:-
Coord C1 exon
chr1:31384261-31384325
Coord A exon
chr1:31383419-31384260
Coord C2 exon
chr1:31383260-31383418
Length
842 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GGTCCCTTGTATTTTGGCAGATT
3' ss Score
6.61
Exon sequences
Seq C1 exon
GCGGAGCCGTCGGAGAGCGCTGCAGCCTGGGCGGAGATCGGGCTGTGCTGCGGCAAGCGGTGCAG
Seq A exon
GTGAGGCTGAGACGGGCAGCGGAGTGATGGCGGGCCGGGATGGGGTGAGCGGGGTCCTTGTTCGAGTATGTAGGCGGTGTGGTGGCTGCTCCAGCCTGCTTTCGGGTGGTGAGGGCCTATAGCTTGCCCGGCCGCGTCTCTTGGGCACCCTCGTGGGGATGGGCAGGTGGAGAGCGTGAGGGGCGGGTGGGCGGCACCCGGTGCTGCTTCCCTGAGGAGGTGTGGGTCTGGCGGCGGGCTGCAGAACCCAGAGCCGCTCTTCTCACGGGGCTCCTTCTGAAGCGTGCTGCTTTGTCCGCTAGGTGCTAGGTAACGGGACGGGAGGCAGGGAGAGCCGCCTCAGGGTGAGGAAAAACGTACTCGTATTTAAGCATACTTATATTGACAGAAAGTGTGTTTCAGAGTTGGCTTGTCAGGTGCGTTGTTTCTACTCAAGTAAAAGGCAGCGTGTGTATCTTAATCTGTAGTTGAGTCTTAGTCTGAGCATATTGATGTTTTCCTCATTCTGTCTAATGGGAAATGCTCCAGAAATTGCTTTAAACTAAGATGACTGCATCATCATTTCCTGGACTTTTCTTGACCTACTAAATCCCATAATTTACTCTTAAATAGGAGAGCATGACTTATTTTTTGGGTTCTATTTTATCAAAATAATATCTTGACTTTTTGTATTCCCAAATACATTTAACTGCATTTCTTAGTCTCCTCATATTTAATGTTTTTACCAGGCCATTTGAGAAGCATGTCTACTGTGTAAGTCAGATTTCTTTATTTTGAGTTGCTAGCTTCCTTCAGTATGTGCTTACAAATTCTCCTTAGGAAGGTCCCTTGTATTTTGGCAG
Seq C2 exon
ATTACAATGACTGCATCAAATAAAGCACTGGAGCTTCAGCTGCAGATGAAGCAAAACGCTGAGGAACTGCAGGATTTTATGAGGGAATTAGAGAGCTGGGAAAAGGATATTAAAGAAGTTGATTCAGAATTAAGGAAACAGAGTGGTGTCTCAGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009743:ENSGALT00000015853:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.675
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF138631=DUF4200=PU(92.5=96.1),PF075448=Med9=PU(96.0=94.1)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion 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:
GAGATCGGGCTGTGCTGC
R:
CTCTTCTGAGACACCACTCTGT
Band lengths:
191-1033
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]