GgaINT0080062 @ galGal3
Intron Retention
Gene
ENSGALG00000016565 | F1N9F1_CHICK
Description
NA
Coordinates
chr3:107878164-107878439:-
Coord C1 exon
chr3:107878395-107878439
Coord A exon
chr3:107878274-107878394
Coord C2 exon
chr3:107878164-107878273
Length
121 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CCCTCCTTGCCTCCTTCCAGGAA
3' ss Score
11.95
Exon sequences
Seq C1 exon
GATGAGAAGAACCAAATGATGACCACAAATGTTTGGCTGAAGCAG
Seq A exon
GTAGGAGTCTGTGCCCTCCATGGGGCCTGGGTTGGAGAGATCAAGAAGGAGGAGGACGGTATGGGGCAGCTCAGTCCTACCAGACCCAGGGTCACCTGGTGCCCTCCTTGCCTCCTTCCAG
Seq C2 exon
GAATGGAGTGACTACAAGCTGCGCTGGAACCCAGAGGACTTTGACAACGTCACCTCCATCAGGGTGCCCTCTGAGATGATCTGGATCCCCGACATCGTGCTCTACAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016565:ENSGALT00000026738:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(6.8=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(17.4=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:
ATGAGAAGAACCAAATGATGACCACA
R:
TTGTTGTAGAGCACGATGTCGG
Band lengths:
154-275
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]