RnoINT0107672 @ rn6
Intron Retention
Gene
ENSRNOG00000013670 | Pax3
Description
paired box 3 [Source:RGD Symbol;Acc:620431]
Coordinates
chr9:84099294-84101172:-
Coord C1 exon
chr9:84100704-84101172
Coord A exon
chr9:84099530-84100703
Coord C2 exon
chr9:84099294-84099529
Length
1174 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGT
5' ss Score
10.75
3' ss Seq
CTTTCGCCTTCTCTTCCCAGTGT
3' ss Score
9.92
Exon sequences
Seq C1 exon
TCCCTCGTCGGGATCCCTGCACTCCGTGTCAAGGCGGGAGGAGACTTGGGACGTACTCCTGCCTCGTCACCACCCTCCCTCCCCCGATCTTCGCGGTGCCTTGAGCACCTTTGCCAGTGGCCCCAGCTGAGGGGCCGATCTGCTAGACTCGCACCAAACTTGTCCGCCCTGGGCTTGGGATCCTGCACTCAAGGGACTCCTCTGGAGCCAGTGGACTTGGAGCTATTAGCGCCCCCTCCCCGCGCCCCGCCTCCCTCTCCTGCCTTTTTTTGGGGAGGAGCTCTCCGCGATCCGGAGAGTTCCCGAGGGTCACCCGCCGCACTGTGCTCGCTTTTCCGTCTCGCCTTCACCTGGATATAATTTGCCAGCGAAGCTGCCCCCAGGATGACCACGCTGGCCGGCGCTGTGCCCAGGATGATGCGGCCCGGCCCGGGGCAGAATTACCCACGCAGCGGCTTCCCACTGGAAG
Seq A exon
GTACGTTAGGGCCTCAGCTCATCCGGATCCTGGGGCCTGGGATTGGCTGCCGCACCCCAATCCTAGTCTCCGGGGCCTCCGGTCGTGCGTTACCCTCAGCCTCTTCCCTTGGTACTTCCCAACCCCAGAAGCAAAAGTGGGGAGGGGGTTCTCGAGGAGAGCGGGAGAAGCCCCATTTCGCGTTCTGGCTGCAAACGGAGCACTATGCTCACTCCAAGGTCTTGGAGCTTGCCTGGCCTGCTTCGGCCCGCTCCACTTTGCTGGGCTGTTTTGGAGTTACTGCCGCGAGAAAGGTGGACAAGCTTCGCAGCGCCGGAAGCAAGTTCTCTTTTTGTCCACCAAAAGTTGCTACGAAACATTTCCGGCTGCGTTCACCTTGGAATAACTCCTGTTAGTTCGTCAAGAATTTTCCTGCTGTAAAAAATTGAGGTGGCCCTTCCTAATTGAAAGTTTTTAGCACTGATTAGTTAAATGCCATTAAACTCAAGTGGCATCTCGAAGTTTCTAAAATATTTGGCAGTGGCGCTCCGGTTCGCTTGAAGGTGCTGGGAAATTTCGGGGGAGGTAGAAATCGTTGCAAACACGAACCCGACCAATACTCTTAGGAAAAGCCTGGGGTTCTGGAGGAGCCCTTCCGCCTCGATCCAAAGTAAAATGCAAAGTGTAAGAGCAGTTATTTCGGCTGTGGTGTCCACAGCTAGGCTCGCTGCTGTTTTTTAGTTCTGAAGTGTAACAGGTGATACATGCTGTCACCTGTGTCTCCTTTCGGGAGCCTTCCGACCCTTGTTTACTACACTCTGATCCGGAAACACTAAAGACCTCTCAGGATTTTGAGACAGCCATTGCAAGACATTTTAGACATCAGCCCTATGTCTCCCTCCACTTTGCAGCACCCCCTCTCCCCCCCCAAAAAAGAGAAAATACAGTTTCTCTGCAGCCTTTATCTCGGAGCCAATCGCTTGATTCCCAAAAAATTATATGCCCCTGCATTGGATAATTATTTAAATAAATATAATCTTAAAGGTCCGGGAGTAGGAGTCCAAAGCCTGGTGGTTTGTGTTTAACTGTCACAGGCGAATTGGCCAGAAGGACGCAGAATCAGGTTCTTTCTGCTGCTTTCTGTTCTTCCTAAATGACTTTCCCCTGGGCTCTTTCTTTCGCCTTCTCTTCCCAG
Seq C2 exon
TGTCTACACCCCTCGGCCAGGGCCGAGTCAATCAGCTCGGAGGAGTATTTATCAACGGCAGGCCTCTGCCCAACCACATCCGCCACAAGATCGTGGAGATGGCCCACCACGGCATTCGGCCTTGCGTCATCTCTCGCCAACTTCGCGTGTCCCACGGCTGTGTCTCTAAGATCTTATGCAGGTACCAGGAGACAGGCTCCATCCGACCTGGCGCCATTGGCGGCAGCAAGCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013670:ENSRNOT00000018652:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (disopred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0029213=PAX=PU(57.9=92.4)
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:
AGCCAGTGGACTTGGAGCTAT
R:
GATCTTGTGGCGGATGTGGTT
Band lengths:
356-1530
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]