RnoINT0107685 @ rn6
Intron Retention
Gene
ENSRNOG00000008020 | Pax4
Description
paired box 4 [Source:RGD Symbol;Acc:620433]
Coordinates
chr4:55737647-55738159:-
Coord C1 exon
chr4:55738077-55738159
Coord A exon
chr4:55737717-55738076
Coord C2 exon
chr4:55737647-55737716
Length
360 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
CAGTCCCTGTTCTCTCTCAGGTC
3' ss Score
9.01
Exon sequences
Seq C1 exon
AGTTCCAGCGTGGGCAGTATCCAGATTCAGTTGTCCGTGGAAAGCTGGCTGCTGCCACCTCTCTGCCTGAAGACACAGTGAGG
Seq A exon
GTGAGTGAGCTCTGGAACACAGTGTGAGGAAACAGTAAAGGAGAAGAATGTACTGATCATGGCTTGAGGTCTGTGGAGGCAGAGATGGCAACAAGAGGGTGGAAAAACTTGTTTGAAAAAAAATAAAAAGAGAGACGAAATCCTCCCTGCTTTCCTGCCAATTTCTCTCTCTTCTTTCCCCCACCCGAGCCTTTTAGGTGAGGAAAAAGACAGAGAGCAAAGAAAGGCCTGAGCAGTGGGTGAGGGTGTCAGAATGGAGGGAGACTCTACTTTCTGAGTCCAAGCAAGGGACACACGGTAAGAGCAACTGGTGCCAGGTGACTGAAAACGCAGTCAGTAACAGTCCCTGTTCTCTCTCAG
Seq C2 exon
GTCTGGTTTTCCAACAGAAGAGCCAAATGGCGCAGACAAGAGAAGTTGAAATGGGAAACACAGATGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008020:ENSRNOT00000010658:6
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=45.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]