GgaINT0051389 @ galGal3
Intron Retention
Gene
ENSGALG00000012123 | PAX6_CHICK
Description
NA
Coordinates
chr5:5257658-5258041:-
Coord C1 exon
chr5:5257891-5258041
Coord A exon
chr5:5257774-5257890
Coord C2 exon
chr5:5257658-5257773
Length
117 bp
Sequences
Splice sites
5' ss Seq
CCGGTAATG
5' ss Score
6.21
3' ss Seq
ATCTGTCTATTCTATTATAGTTT
3' ss Score
8.19
Exon sequences
Seq C1 exon
GTGTGGTTTTCTAACAGAAGGGCCAAGTGGAGAAGGGAGGAGAAGCTGCGGAACCAGCGGAGACAAGCCAGCAACACTCCCAGCCACATCCCCATCAGCAGTAGTTTCAGCACAAGCGTTTACCAGCCGATCCCACAGCCGACCACCCCCG
Seq A exon
GTAATGCAGCCAACCCACCCGCGTGAAGCCATCCTCGGGACACCGAGACCGTGGGACTGTGCCACCGAGCGCGATGGTTAAACTAATGTCTCCATCTATCTGTCTATTCTATTATAG
Seq C2 exon
TTTCCTCTTTCACATCAGGTTCCATGTTGGGCAGGACAGACACAGCGCTCACGAACACGTACAGCGCACTGCCGCCCATGCCCAGCTTCACCATGGCCAACAACCTGCCTATGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012123:ENSGALT00000019804:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.904 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=21.6)
A:
NA
C2:
NO
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:
ACAGAAGGGCCAAGTGGAGAA
R:
ATAGGCAGGTTGTTGGCCATG
Band lengths:
250-367
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]