DreINT0110588 @ danRer10
Intron Retention
Gene
ENSDARG00000103379 | pax6a
Description
paired box 6a [Source:ZFIN;Acc:ZDB-GENE-990415-200]
Coordinates
chr25:14935346-14935803:-
Coord C1 exon
chr25:14935653-14935803
Coord A exon
chr25:14935459-14935652
Coord C2 exon
chr25:14935346-14935458
Length
194 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
CATTTTTATCCTTTAAACAGTAT
3' ss Score
6.97
Exon sequences
Seq C1 exon
GTCTGGTTCTCAAACAGAAGAGCGAAATGGAGGAGGGAGGAAAAGTTAAGAAATCAAAGAAGACAAGCCAGTAATTCCTCAAGTCACATACCCATCAGCAGCAGCTTCAGCACAAGTGTCTATCAACCAATCCCTCAGCCCACAACGCCAG
Seq A exon
GTAAACGCTTGAAAATGATTGATAAGCAAATACTATTTTAATAAAGCAAACATTATTTAATCAAGTGCAAATTTGGGTTGACTGGGACATTGTTTTCCAGTCATCTCAATGGCAAAAGTGTCCCAATCTACTCGAATGCACCCACTACTTCTAATAAGCAAGATACTAAGTGTGCATTTTTATCCTTTAAACAG
Seq C2 exon
TATCCTTTACGTCAGGCTCCATGTTGGGCAGATCAGACACAGCTCTTACGAACACATACAGCGCCCTGCCACCAATGCCAAGCTTCACCATGGCCAACAACCTTCCTATGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103379:ENSDART00000164384:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=21.6)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGAGCGAAATGGAGGAGGGA
R:
GCATAGGAAGGTTGTTGGCCA
Band lengths:
245-439
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]