DreINT0110597 @ danRer10
Intron Retention
Gene
ENSDARG00000103379 | pax6a
Description
paired box 6a [Source:ZFIN;Acc:ZDB-GENE-990415-200]
Coordinates
chr25:14937543-14938233:-
Coord C1 exon
chr25:14938075-14938233
Coord A exon
chr25:14937626-14938074
Coord C2 exon
chr25:14937543-14937625
Length
449 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAC
5' ss Score
8.14
3' ss Seq
TTTTTGTTTGTTTCCACCAGAGT
3' ss Score
8.93
Exon sequences
Seq C1 exon
ATGGTTGCCAACAGTCAGACGGAGGCGGTGAGAACACAAACTCAATAAGCTCCAATGGCGAGGACTCAGATGAGACCCAAATGAGGCTTCAGCTTAAACGAAAACTGCAAAGGAATCGCACTTCTTTCACACAAGAACAAATAGAAGCACTTGAAAAAG
Seq A exon
GTAAACATGGAGATTATAGCGAATATTACAGCATCTGTTACAAACTAACAAAATAATTAGGAACAATATAACTTGTTGAAATGTGGCTAGTTTAATATATGTCCTTAAAAGAATTGATTAATATTCTTATGTTCTGTATTCCAGATTCAAACTTGTATGCATTTGCAATAAAGTGATGATTTATGTTTATACGTAACTATTTGTGCTTAAGATAAAAGATTTTAATATAATAAACTATTTATACTAAACTAAAATATACTAAATATTTATGGTTCATTTTTAAAAAATATCAATAGCAAGTGTGTTTAAGCCATATTAATTATTTGTAATAAACTAATCAAATGCGGACATTTAAGTTACCCGGCCCTAAAAAATATCAAATATTTAACTTTTTTGCCCAATATTGTAGCATTTTCAAAATGTTTCCTATTTTTGTTTGTTTCCACCAG
Seq C2 exon
AGTTTGAAAGAACGCACTACCCTGACGTTTTTGCACGAGAAAGACTTGCTGCAAAAATAGATTTACCAGAAGCAAGAATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103379:ENSDART00000164384:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.699 A=NA C2=0.697
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(43.6=31.5)
A:
NA
C2:
PF0004624=Homeobox=FE(47.4=100)
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:
ATGGTTGCCAACAGTCAGACG
R:
CTGTATTCTTGCTTCTGGTAAATCT
Band lengths:
242-691
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]