GgaINT0051388 @ galGal3
Intron Retention
Gene
ENSGALG00000012123 | PAX6_CHICK
Description
NA
Coordinates
chr5:5257891-5258370:-
Coord C1 exon
chr5:5258288-5258370
Coord A exon
chr5:5258042-5258287
Coord C2 exon
chr5:5257891-5258041
Length
246 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGG
5' ss Score
10.88
3' ss Seq
CTCAAACGCTGTGCTTCCAGGTG
3' ss Score
7.34
Exon sequences
Seq C1 exon
AGTTTGAGAGAACCCACTATCCCGATGTGTTTGCGAGAGAGCGACTAGCTGCTAAAATAGACTTGCCTGAAGCAAGGATACAG
Seq A exon
GTACGGGGCTGCCACGTAGTTACCGCTGTTATCATTCTTCCTTTTACCACTGTAATTTGTTATGAGTGGCTTCTTGAAGCCGGGTGTAAGGCCGGGTGTTCGCCCATCTCCTCCATCAGGAAGTAGCAGCAGATGGGGTTGGCTTTGCCGTGCCGTGGGGCAGCTCTGCTCTGGCCCTGGGTAACCTGGGGAGCCACGTGCCCTCGCCCCACCGGGCCACTCATGCCTCAAACGCTGTGCTTCCAG
Seq C2 exon
GTGTGGTTTTCTAACAGAAGGGCCAAGTGGAGAAGGGAGGAGAAGCTGCGGAACCAGCGGAGACAAGCCAGCAACACTCCCAGCCACATCCCCATCAGCAGTAGTTTCAGCACAAGCGTTTACCAGCCGATCCCACAGCCGACCACCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012123:ENSGALT00000019804:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.579 A=NA C2=0.904
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(47.4=100)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=21.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGAGAGAACCCACTATCCCGA
R:
GGTGGTCGGCTGTGGGATC
Band lengths:
228-474
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]