RnoINT0107832 @ rn6
Intron Retention
Gene
ENSRNOG00000000440 | Pbx2
Description
PBX homeobox 2 [Source:RGD Symbol;Acc:1303084]
Coordinates
chr20:4358883-4359406:+
Coord C1 exon
chr20:4358883-4358956
Coord A exon
chr20:4358957-4359158
Coord C2 exon
chr20:4359159-4359406
Length
202 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
TCCACTTGCCTGCCTGCTAGGCC
3' ss Score
7.75
Exon sequences
Seq C1 exon
GAAACACGCCCTAAACTGTCACCGAATGAAGCCTGCCCTGTTTAGTGTCCTGTGTGAAATCAAGGAGAAAACTG
Seq A exon
GTATGTGGGTGCCCCTCTGATTCTCACTTCTGGGAGCAGGGCCTCTCTCTACCTTAGGGCTCAGAGTTTGACAACTTGAAGCCCCGAGGAAAGTGAGCGCCACAGAGGCCTCTTGAATGCGAGTGGGGAAAGGGGCGAAGCCTGGAGCCCTGGGTCTTCGAGGAGTTGAGGGGATCCTTAAGTCCACTTGCCTGCCTGCTAG
Seq C2 exon
GCCTTAGCATTCGCAGCTCCCAAGAGGAGGAGCCAGTGGACCCACAGCTGATGCGCCTGGACAACATGCTTCTGGCAGAAGGTGTGGCTGGACCCGAGAAGGGGGGCGGCTCTGCAGCGGCAGCTGCAGCCGCGGCAGCCTCCGGAGGTGGCGTGTCCCCGGATAACTCCATCGAACACTCGGACTATCGAAGCAAGCTTGCCCAAATCCGCCACATCTACCACTCAGAACTGGAGAAGTATGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000440:ENSRNOT00000000509:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.231 A=NA C2=0.651
Domain overlap (PFAM):
C1:
PF037928=PBC=FE(12.6=100)
A:
NA
C2:
PF037928=PBC=FE(41.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACACGCCCTAAACTGTCACC
R:
TGAGTGGTAGATGTGGCGGAT
Band lengths:
299-501
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]