GgaINT0051387 @ galGal4
Intron Retention
Gene
ENSGALG00000012123 | Pax-6
Description
Paired box protein Pax-6 [Source:UniProtKB/Swiss-Prot;Acc:P47237]
Coordinates
chr5:5221375-5222319:-
Coord C1 exon
chr5:5222161-5222319
Coord A exon
chr5:5221458-5222160
Coord C2 exon
chr5:5221375-5221457
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:ENSGALT00000019805:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.994 A=NA C2=0.750
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(29.8=31.5)
A:
NA
C2:
PF0004624=Homeobox=FE(47.4=100)
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:
GCAGCAGGAGGGAGGAGG
R:
GCTTCAGGCAAGTCTATTTTAGCA
Band lengths:
222-925
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]