RnoINT0107706 @ rn6
Intron Retention
Gene
ENSRNOG00000004410 | Pax6
Description
paired box 6 [Source:RGD Symbol;Acc:3258]
Coordinates
chr3:95723107-95723765:+
Coord C1 exon
chr3:95723107-95723265
Coord A exon
chr3:95723266-95723682
Coord C2 exon
chr3:95723683-95723765
Length
417 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACT
5' ss Score
6.64
3' ss Seq
AACAACTTATATTCTTACAGAGT
3' ss Score
6.73
Exon sequences
Seq C1 exon
ACGGCTGCCAGCAACAGGAAGGACAGGGAGAAAACACCAACTCCATCAGCTCCAATGGAGAAGACTCGGATGAGGCTCAAATGCGGCTGCAGCTGAAGCGGAAGCTGCAGAGAAATAGAACATCTTTTACCCAGGAGCAGATTGAGGCTCTGGAGAAAG
Seq A exon
GTGACTGGGAAATTTCCAAAGTAGAGAAACCTTAAATCAAAGTAAATGCCACATCGACAGCACAAAGGGCTAAAATTAGCCAGGGCCCTTTGCATAAAGGCTGAGAAGCCCCCCACCCCCAACTTCTCTGGGTGCGCTGTGCGCTTTCTTTCTTCTTCTCACACACCAGTACTGAGATATTAAAATCCTGATATACAAAGGAAACGATGATCTGGCTGTCTCAGGCCACAGATAAGGGCATTTCCAGCAATATCCTAAATGTCATTCCAAAGAAAACCTAACTGGCTCTGGTGGGAAAGTTCTTGCAAGCACAGTTGGTTGGATGAGATGGGAGTTGGGTGTTAAAAGCTAGCTTGATCCAGAGTTTGGATTATTTTGTATTCTGGCATAACATGGGAACAACTTATATTCTTACAG
Seq C2 exon
AGTTTGAGAGGACCCATTATCCAGATGTGTTTGCCCGGGAAAGACTAGCAGCCAAAATAGATCTACCTGAAGCAAGGATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004410:ENSRNOT00000005882:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(29.8=31.5)
A:
NA
C2:
PF0004624=Homeobox=FE(47.4=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:
CTGCCAGCAACAGGAAGGAC
R:
CTGTATCCTTGCTTCAGGTAGATCT
Band lengths:
238-655
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]