GgaINT0051385 @ galGal4
Intron Retention
Gene
ENSGALG00000012123 | Pax-6
Description
Paired box protein Pax-6 [Source:UniProtKB/Swiss-Prot;Acc:P47237]
Coordinates
chr5:5225498-5226241:-
Coord C1 exon
chr5:5226026-5226241
Coord A exon
chr5:5225664-5226025
Coord C2 exon
chr5:5225498-5225663
Length
362 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
TTCTGTCCTTTGCCTTGCAGGTG
3' ss Score
12.58
Exon sequences
Seq C1 exon
GTGTCGAATGGATGTGTGAGTAAAATTTTGGGCAGGTATTACGAAACTGGCTCCATCAGGCCCAGGGCGATCGGAGGTAGTAAGCCGAGAGTAGCGACTCCCGAAGTTGTAAGCAAAATAGCGCAGTATAAACGAGAGTGCCCCTCCATCTTTGCGTGGGAGATTCGAGACAGATTACTCTCGGAGGGGGTCTGTACCAACGATAACATACCCAGT
Seq A exon
GTAAGTCCACGAGAGAAACCGCTCTGTGTGCTGTGTGGTGCTGGGTAGCTGTAGCCTCTGCCTCCTTTGTTGTGCTATCAGTGAGCGGAGAGCAGGTTCGCATCATTTGCATGTGGCAGGGTCAGGCGCATTTTTTTTTTCATACAGAATCTGACAAATGCCTTTAAGCAGGGGGGGGGAAAACAAGCGACAAACGACGCGGTCATCCCCAGCGCCCGCACCGCGAGCATCAGCCGCAGCGTCGCTCCGGTGGCGCAGCGCGGGGCTCGGGGCCGGGGTCGGGCGTCGGCGGGCGCGGGGCTGCGGGCGGCTCGGGGGCAGCGCTACCGCCCTACCATTGCCTTCTGTCCTTTGCCTTGCAG
Seq C2 exon
GTGTCGTCGATAAACAGAGTCCTCCGCAACCTGGCTAGCGAAAAGCAACAGATGGGTGCCGACGGGATGTACGACAAGCTAAGGATGCTGAACGGGCAGACGGGGACATGGGGCACCCGGCCCGGCTGGTATCCCGGCACCTCGGTACCCGGGCAGCCCGCACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012123:ENSGALT00000019805:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.000 A=NA C2=0.804
Domain overlap (PFAM):
C1:
PF0029213=PAX=FE(51.1=100)
A:
NA
C2:
PF0029213=PAX=PD(5.8=14.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTCGAATGGATGTGTGAGT
R:
CCATGTCCCCGTCTGCCC
Band lengths:
327-689
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]