RnoINT0107836 @ rn6
Intron Retention
Gene
ENSRNOG00000000440 | Pbx2
Description
PBX homeobox 2 [Source:RGD Symbol;Acc:1303084]
Coordinates
chr20:4360078-4360618:+
Coord C1 exon
chr20:4360078-4360231
Coord A exon
chr20:4360232-4360529
Coord C2 exon
chr20:4360530-4360618
Length
298 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
TCTCTCTCTGCCCTCCCAAGGCT
3' ss Score
7.75
Exon sequences
Seq C1 exon
GTTTCCAACTGGTTTGGTAACAAGCGGATCCGCTATAAGAAAAACATCGGGAAGTTCCAAGAGGAGGCAAATATCTATGCTGTGAAGACAGCCGTGTCCGTCGCCCAGGGCGGCCACAGCCGCACCAGCTCTCCAACGCCCCCTTCCTCTGCAG
Seq A exon
GTACAGCTCACTGCCGCTCTGGCTGGCTGCTTTGCCCATTTGCTGCCTTTGCTTCCACTTTTGTCCATGCAGGACTTTGGGGGGGTGAAAGACCAGGCTAAGACGGGGTGGTGATGTCAAGGGCCTTAAGTGGGTAGCCAGTTCACGTTCACGAATAGCCTGTCCTGAGGGTGGGCCTGTGGATAGTCTGCATATGCTTCCTGAGTGAGCTTTCTGGAAGCCAAGGGTTGGATTTACCTCCTGTCCCTCATCAGGGTGCCCTGTGCTTTTTCTCTGATTCTCTCTCTGCCCTCCCAAG
Seq C2 exon
GCTCTGGCGGCTCTTTCAATCTCTCAGGATCCGGAGACATGTTTCTGGGGATGCCCGGGCTCAATGGAGATTCCTACCCTGCTTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000440:ENSRNOT00000000509:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.327 A=NA C2=0.500
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=25.0)
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:
TCCGCTATAAGAAAAACATCGGGA
R:
TGGGAAGCAGGGTAGGAATCT
Band lengths:
214-512
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]