GgaINT0051385 @ galGal3
Intron Retention
Gene
ENSGALG00000012123 | PAX6_CHICK
Description
NA
Coordinates
chr5:5262411-5263154:-
Coord C1 exon
chr5:5262939-5263154
Coord A exon
chr5:5262577-5262938
Coord C2 exon
chr5:5262411-5262576
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
GTGTCGTCGATAAACAGAGTCCTCCGCAACCTGGCTAGCGAAAAGCAACAGATGGGTGCCGACGGGATGTACGACAAGCTAAGGATGCTGAACGGGCAGACGGGGACATGGGGCACCCGGCCCGGCTGGTATCCCGGCACCTCGGTACCTGGGCAGCCCGCACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012123:ENSGALT00000019804:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.005 A=NA C2=0.817
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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAGGTATTACGAAACTGGCT
R:
CTGCCCAGGTACCGAGGTG
Band lengths:
342-704
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]