RnoINT0107839 @ rn6
Intron Retention
Gene
ENSRNOG00000022162 | Pbx3
Description
PBX homeobox 3 [Source:RGD Symbol;Acc:1307198]
Coordinates
chr3:13434881-13435979:-
Coord C1 exon
chr3:13435778-13435979
Coord A exon
chr3:13434955-13435777
Coord C2 exon
chr3:13434881-13434954
Length
823 bp
Sequences
Splice sites
5' ss Seq
AAAGTTGGT
5' ss Score
1.99
3' ss Seq
TTTTGCTGTTTGTTTTTTAGGAA
3' ss Score
13.16
Exon sequences
Seq C1 exon
GGATGGACGATCAATCCAGGATGCTGCAGACTCTGGCCGGGGTGAACCTGGCCGGCCACTCGGTCCAAGGGGGTATGGCTCTGCCGCCTCCCCCTCACGGCCACGAAGGGGCGGACGGCGACGGCAGGAAGCAGGACATCGGCGACATCCTCCACCAGATCATGACCATCACCGACCAGAGCTTGGACGAGGCGCAAGCAAA
Seq A exon
GTTGGTGTCGTCTCATTAAGCATCTTTTGTGTGTGTACGGGAGCCGGGCTCGGGTCCCGGGTGGTTCCCGGGACCGGGGCCTCAGTCTCGGGCGGGAACTTTCTCCGCCCGCCGGGCACTTGCCGAGTCCTCCATCGCGCGGGCAAAGTTGCTCGCCGGGTTCGGGACAAACTCGATCAGTGCTTCGTCCGTGCCCCGCTGCCCGGCCCCCTCCCCGGATTTAAACATCCCGCCCGGGCCCCGGTGCGCTCCGCGTCCCTGCCGGGTCCCGGACCGCACCGCCGGGAAGTGCAACTTTCTCCGCCCGCCCAGACTCCGGGCATCCACTCCCCTCGGCCCAGTCCGGGGTGACCGGCTGCTTTCCCCCACGTCCCTGTGCGGGAGCGCCAAGTTCTCTAGGAGGGAGGGCCGCTTGGCAAACTTTGCGGAGCTGTCACCCGCTGATTATCAGCCGCCGGCCGGCCGCTGCGCCCGCTGCTCCTGTGGAGCTTGGGCGTTGGGGTCCCCTCCGCGTCGGTCTGGTCCCTTGGGTCACCGCCGCGCTCCCCGGAGCGGAGCCTTATGAGCGGGTCACTCCTGCGTCTGCCGAGGCTTCTGTCGGCCCAGCAGATGGGTCACGCTGCTATCGGGCTGAAGCTCTCGCCGCTAGAGCTTGCAGCCAGTTGCGAACTAGTCAACTTGAGTTTTGTTGACTTCCCGTGGTTCAAAAGAGCTTTCCCAAATAGGGGGCCGGTTTTAAATCTTGGGTCTAACTTAAAGGAAGGCGCCATATTATTCCAATAGGTGATGCTAATACCTTTGTGTTTTGCTGTTTGTTTTTTAG
Seq C2 exon
GAAACATGCTCTGAACTGTCACAGAATGAAACCGGCGCTCTTCAGCGTCTTGTGTGAGATCAAAGAGAAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000022162:ENSRNOT00000029600:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.847 A=NA C2=0.192
Domain overlap (PFAM):
C1:
PF037928=PBC=PU(14.7=43.3)
A:
NA
C2:
PF037928=PBC=FE(12.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGACGATCAATCCAGGATGC
R:
TTTTCTCTTTGATCTCACACAAGACG
Band lengths:
270-1093
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]