GgaINT0051387 @ galGal3
Intron Retention
Gene
ENSGALG00000012123 | PAX6_CHICK
Description
NA
Coordinates
chr5:5258288-5259232:-
Coord C1 exon
chr5:5259074-5259232
Coord A exon
chr5:5258371-5259073
Coord C2 exon
chr5:5258288-5258370
Length
703 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
GGCAATATTTCTCCTTGCAGAGT
3' ss Score
8.22
Exon sequences
Seq C1 exon
ACGGCTGCCCGCAGCAGGAGGGAGGAGGGGAGAACACCAACTCCATCAGCTCCAATGGGGAAGATTCCGATGAGGCCCAGATGAGACTTCAGCTGAAAAGGAAGCTGCAGAGAAATAGGACATCCTTTACCCAAGAGCAAATCGAAGCCCTTGAGAAAG
Seq A exon
GTGAGTGACATTTTGCTGCCGCCGCGGTAGGGGAGAAAGGCAAGAGACACCCTAGCTGCATTAGGAGCTGAGCAGATTCCTGGCATTCACATGCCTTGTAGAGATACGGACAGCTCTGAGGCCCCTGGCTCCTTCCATGCCATTTCATTCTGACCCCCATCGATGGCTGCGGAGAACAGAAAGGGCAGCGCAGGGCACAGTGCAGTGCTGCACCCCAGGCTGCCCTCCTCCTGCTGGGTGGTGGTGGGGCAGGGTACCAGCAGGGCAGGGTGCTGGATGCTGGCAGGACAGGGTGCTGGGTACAGGCAGGACTGGGTGCTGGGTGCCAGCACCATGCTCGCTCCCCATCCTCAGTGCTGCTGCTGCCCAGGGCTGGCAGCCGGTGCCCTTCTCCCCAGCCGTGGCCGGCTCTCTGCCCAGATTTCCTGCCGTCATGCGGCCACGTGCCACTCAGCTTCTTGGTCATGGGGTCAGGGTGCCATGGGAGCTCCTCACAGGGGTAAGAAGATCATGCCCAGCCCCAGCCCCACCGTGTCCCACAGCCTGGGGTCCTTCCCAGCACACATTTATACAGGTAGCTCAGTGCTGTCTCGCAGCACTGATTCTTGCAGGCACTGAGGGTGCGGCTGTGCCACAGGGCTGGGACTTGACCATCAGCCACATTCGTTCTCTGCAGCTCACACGGCAATATTTCTCCTTGCAG
Seq C2 exon
AGTTTGAGAGAACCCACTATCCCGATGTGTTTGCGAGAGAGCGACTAGCTGCTAAAATAGACTTGCCTGAAGCAAGGATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012123:ENSGALT00000019804:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.920 A=NA C2=0.579
Domain overlap (PFAM):
C1:
PF0029213=PAX=PD(1.6=8.7),PF0004624=Homeobox=PU(29.8=73.9)
A:
NA
C2:
PF0004624=Homeobox=FE(47.4=100)
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:
GCAGCAGGAGGGAGGAGG
R:
GCTTCAGGCAAGTCTATTTTAGCA
Band lengths:
222-925
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]