RnoINT0107707 @ rn6
Intron Retention
Gene
ENSRNOG00000004410 | Pax6
Description
paired box 6 [Source:RGD Symbol;Acc:3258]
Coordinates
chr3:95723683-95724110:+
Coord C1 exon
chr3:95723683-95723765
Coord A exon
chr3:95723766-95723959
Coord C2 exon
chr3:95723960-95724110
Length
194 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCT
5' ss Score
8.16
3' ss Seq
CCTGTTCCATGCATTTCCAGGTG
3' ss Score
11.27
Exon sequences
Seq C1 exon
AGTTTGAGAGGACCCATTATCCAGATGTGTTTGCCCGGGAAAGACTAGCAGCCAAAATAGATCTACCTGAAGCAAGGATACAG
Seq A exon
GTACCTGGGGACCATGTTGGGTTTGTGTGTTGTGGGTACTTATCTTTTGCCTTGCCTGTATGCCAGTCATTGATATAAACAGGGTTAGCTTGCAAAGACTCCCTGGTCCTAGGGCAAGGATGGGAATGGAGGGGTTTTTGTTTGCAGCAGGGCTGGTAGCAAGCACAGGGCTAACCTGTTCCATGCATTTCCAG
Seq C2 exon
GTGTGGTTTTCTAACCGAAGGGCCAAGTGGAGAAGAGAAGAAAAACTGAGGAACCAGAGAAGACAGGCCAGCAACACCCCGAGTCACATCCCTATCAGCAGCAGTTTCAGTACCAGTGTCTACCAGCCAATTCCACAGCCCACCACACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004410:ENSRNOT00000005882:8
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=FE(47.4=100)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=21.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTTTGAGAGGACCCATTATCCAGA
R:
CAGGTGTGGTGGGCTGTG
Band lengths:
234-428
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]