RnoINT0107845 @ rn6
Intron Retention
Gene
ENSRNOG00000022162 | Pbx3
Description
PBX homeobox 3 [Source:RGD Symbol;Acc:1307198]
Coordinates
chr3:13245413-13246402:-
Coord C1 exon
chr3:13246290-13246402
Coord A exon
chr3:13245503-13246289
Coord C2 exon
chr3:13245413-13245502
Length
787 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CTGTTTCATCTCACTTCTAGGTG
3' ss Score
11.91
Exon sequences
Seq C1 exon
GTTCTTCTGGTTCTTTTAACCTCCCAAATTCTGGGGACATGTTCATGAACATGCAGAGTCTGAATGGGGATTCTTACCAAGGGTCCCAAGTCGGAGCCAATGTGCAGTCACAG
Seq A exon
GTAGGAGAAATGCCCCAGCTGGGGCCTTTCTGGCAGGGTAGGGTTTGGGTTCAAAACTCCCCGCTCTGACCCGTGAAAGTGGTCTGCACATCTATGCAGCACCTGTGCTGGGCATCCAAACGGGACACGTTTGCCCACCTCTTAATTCAGTGAGAAGTTAAGCGAACAATGCCTTTGATGATTCAAAGCTGACGAACTTTGTGAATGCATTCGGCTCTGGCTTGAGCTCATGGAGATGGGGGAGGGGGCCTTTGTCATGACAGAACAGAAGATTGTGTGTGCCTGAGAAAGGGAAGGGGTGGGAAAAGAGGGAAAGGGAAAGAATAAACAAGAGAACATATTGTTCTTTTATTCCCGAATGCTTGCAAGTCAGGACACTGAAACCTGAACTCCTAAAATAGATCCCAGGTTGAACCCCTTTCTCGTCCTTTTGACTGAGAGCAAGTACTCTCTCGCTCTTATGCACTGGTGGTGGGGACGGGCTGGGGTTCAGCATTCGTTACCAGTGAGTAGGTTTCCACCCACAGCCACACACACTTGGTTGCTGTAGATGGAAAGTCTGCGTTACCATGAAGATGCTATTGTTTGGCTGGTGTGAAAAACAAAGATGTGTGAGTTTAAATATGCAAGGAATCTTTGAAATCCCTCCAGTCACATCTGATTGATAAATTTGTCTTTCATTGAGGATGCTCCACCCTTGTGGCACACATAACTCAAATTGTTCCCTTTGTAAGTGATGATGTTTTAATAGATGGAGGTGATGAATTCTGTTTCATCTCACTTCTAG
Seq C2 exon
GTGGATACCCTCCGTCATGTTATCAATCAGACGGGAGGCTACAGTGACGGCCTTGGAGCAAACTCACTGTACAGTCCGCATAACTTAAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000022162:ENSRNOT00000029600:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.789 A=NA C2=0.933
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GTTCTTTTAACCTCCCAAATTCTGG
R:
AAGTTATGCGGACTGTACAGTGA
Band lengths:
190-977
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]