DreINT0110595 @ danRer10
Intron Retention
Gene
ENSDARG00000103379 | pax6a
Description
paired box 6a [Source:ZFIN;Acc:ZDB-GENE-990415-200]
Coordinates
chr25:14942079-14942740:-
Coord C1 exon
chr25:14942525-14942740
Coord A exon
chr25:14942245-14942524
Coord C2 exon
chr25:14942079-14942244
Length
280 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
TCTTTGGGTTCGTCTTTCAGGTG
3' ss Score
11.59
Exon sequences
Seq C1 exon
GTGTCCAACGGCTGCGTGAGTAAAATCTTGGGTAGATACTATGAAACAGGCTCCATCAGACCCAGGGCGATCGGAGGAAGTAAACCACGAGTAGCGACTCCCGAGGTGGTCGGCAAAATTGCCCAGTACAAGAGGGAGTGTCCGTCAATCTTCGCGTGGGAAATCCGAGACAGGCTGCTATCAGAGGGGGTCTGCACAAACGATAATATACCCAGT
Seq A exon
GTAAGTTGATTCAGTGAAGTTGCCATGAATTCATTAACAACATTAATGTAGAGATATTTTATGCATTTCTTGACGCAAGCATTAATGACCTTGAACGTGAACATTCTCCAACATCGGCCACTGCTGTAACCTCCTCTTTGCCAGAGGACAATGCAATGCGATGTAATGCTCTGGCATGTAGGCCTGTGCAGAAATGGGGCCAATCGTTCCAAAAGCCAAGATGCCACATCGCGGACGCGCTCTTTAATTAATGTGCCGCATCTTTGGGTTCGTCTTTCAG
Seq C2 exon
GTGTCATCGATAAACAGAGTACTGCGCAACCTGGCTAGCGAAAAGCAACAGATGGGCGCAGATGGCATGTATGAAAAGCTGAGGATGCTGAACGGTCAGACCGGCACGTGGGGGACCCGGCCGGGCTGGTACCCCGGAACCTCGGTGCCAGGACAGCCCAATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103379:ENSDART00000164384:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.004 A=NA C2=0.642
Domain overlap (PFAM):
C1:
PF0029213=PAX=FE(56.8=100)
A:
NA
C2:
PF0029213=PAX=PD(6.4=14.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGGCTGCGTGAGTAAAATCT
R:
CCGTTCAGCATCCTCAGCTTT
Band lengths:
304-584
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]