RnoINT0107844 @ rn6
Intron Retention
Gene
ENSRNOG00000022162 | Pbx3
Description
PBX homeobox 3 [Source:RGD Symbol;Acc:1307198]
Coordinates
chr3:13246290-13247875:-
Coord C1 exon
chr3:13247710-13247875
Coord A exon
chr3:13246403-13247709
Coord C2 exon
chr3:13246290-13246402
Length
1307 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CTTAACTCTTTCCTTTCCAGGTT
3' ss Score
11.89
Exon sequences
Seq C1 exon
GTATCCAACTGGTTTGGCAACAAACGAATCAGGTACAAGAAGAACATCGGCAAATTTCAAGAGGAGGCCAATCTCTATGCTGCAAAAACAGCCGTGACAGCCGCACACGCAGTGGCCGCAGCCGTGCAGAACAACCAGACCAACTCACCCACCACGCCAAACTCTG
Seq A exon
GTGAGTATGGCATGCGCACTCCCTACGCAGCCAGACAGGCATCTGCCACAGGCTCTGAAGCTTCAGCCTCACTGGGTGCACAGTGGGCCTTTCAGGAGAGATTTGTATTCGCTTATAGGCTTGTTCTGGAGATGGGTAGATAAGGGGCCAGCCTGTGCTGGGAAACCCACTGTTCACAGCGAATGCCACTCGCTCCTGTAGATGCTAGAACCTTTATACTCAGCCATGGCCTTTAATTCAGCAGATACGCAAAGTTCTATCATATAATGTTCCGCCTATCACCTTAGGGTCATTGGTGGTCTGTCAGACTGAAGCAGCAGGTATGTACTGGTTGGTAGGGAAGCTGAATGCTGGGTTGGGACGTTGCTGTGCTTCCTGTGCTCTTGGCTTCAGGCTCTAGGTCGCAGCCTGTCTGTGCCAGGTGACTTGCTGAACTTGCATATAAAGGAATGATTTTTTTGTTTTGTTTTTGTTTTTTGTGGTAGTGGGGCTTAAACCCGGGGCTTTGCATATGCAAAGTTTATGACTAGCCATTATTTTTTAAAGATAGTCTTACTAAGTTGTCCAAAAAAGCCTTGAACTCACTTTGTAGCTGTCTGCCCTCAAACTTGTGATTCCTCTGCCTCAGCTGACTAGGTGGGATTGCATGTGTGTGCCACCACAGCTGGCTATAAATGCACTATTTTTGACTCCTTACACAGAACATTCCATTTAAATTTTATGTGGCATTCATGGAGTTTGAAGAATGTCTTTAAATTACAGGGAACTTGGCTGGCAGCGGAAGGTGCAGCTAACCCTAGTAGAAGAGTTGGAGGGCCTCGGATGCTTTCTAGGGAGATTTTAAAATATACATTTAAAGGTCCAGGGAAGGTTGTCTGTTTTATTATACCCCCATCATTTCTACTGGGCCACAGACACTGGTGAGTGGAAACATAGAGTTATATCTAGGAGAAAGTGTCAGGAAAGTGTCTTCTCCAGGTAGTTCTCCACCATGACACTGAACATTGAAGAGCTTGTTTGATTAAGTCTGGAGAGAAATGGAAACAAGGAGAAGGCTGGGGCCAGCTCCTGGGTGCTTTCTGCCTATTTTGATTCGTTTCTGGTTTTTCACTTGGGTTCACCCTCTATAATGTTCTTCCTGTGTATAGTGTGAGTAGCAGGACCTTCTAGAGCTGAGTTAACGTTCTGTCCTTCTAAAGCTGGAAATGCCTCTCCCTTCTGCCTCTTTTCCTTTCCCTACCTCGAGGTCTTTGGGGATTGTGTATGTAGCTCTCTGTTATTCAGCTACTTAACTCTTTCCTTTCCAG
Seq C2 exon
GTTCTTCTGGTTCTTTTAACCTCCCAAATTCTGGGGACATGTTCATGAACATGCAGAGTCTGAATGGGGATTCTTACCAAGGGTCCCAAGTCGGAGCCAATGTGCAGTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000022162:ENSRNOT00000029600:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.330 A=NA C2=0.789
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=23.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAACAAACGAATCAGGTACA
R:
GTGACTGCACATTGGCTCCG
Band lengths:
262-1569
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]