GgaINT0144667 @ galGal3
Intron Retention
Gene
ENSGALG00000001842 | F1NFQ7_CHICK
Description
NA
Coordinates
chr28:2241737-2242181:-
Coord C1 exon
chr28:2242021-2242181
Coord A exon
chr28:2241882-2242020
Coord C2 exon
chr28:2241737-2241881
Length
139 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCCTCACAGCTCCCCCGTAGGCG
3' ss Score
3.96
Exon sequences
Seq C1 exon
CCACCAGGTGCTCACAGCAGTTGGGTCATCGGGGGAAAGGCAGCGGTGCCGCACTCGCGGCCCTTCATCGCCTCCATCCAGATGGACGGGCAGCACTTCTGTGGGGGGTTCCTGGTGTGGCCCAGGTGGGTGATGACAGCCGCCCACTGCCCTGTTCCCAG
Seq A exon
GTGAGCGGTTTCCCCCGGGTCCCATTCACGTGGATACCCCCACCCCGGAGCAAACCCCCTTTGCTCAGCTCTCTCCCCAGGCTCCCCATCCCCTCTCCCCCTTTGGGGGCTCCCATCCCTCCTCACAGCTCCCCCGTAG
Seq C2 exon
GCGCGAGCCCTCCGTCCGCGTGGTGCTGGGAGCGCACAGCCTGGAGCAGCCCGAGGAGTCCCAACAGGTTTTCGGTGTCGAGGAATCCATCGCGCATCCCCTCTACAACCCCCGGACGGTGGACAACGACATCCGCATGCTCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001842:ENSGALT00000002851:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.061
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=PU(23.9=84.9)
A:
NA
C2:
PF0008921=Trypsin=FE(25.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCACAGCAGTTGGGTCATCG
R:
CGATGGATTCCTCGACACCGA
Band lengths:
243-382
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]