GgaINT0138231 @ galGal3
Intron Retention
Gene
ENSGALG00000007406 | F1N9M8_CHICK
Description
NA
Coordinates
chr24:5557777-5558199:+
Coord C1 exon
chr24:5557777-5557936
Coord A exon
chr24:5557937-5558032
Coord C2 exon
chr24:5558033-5558199
Length
96 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
AGTAACGTGTCCGTGCGCAGGAA
3' ss Score
7.66
Exon sequences
Seq C1 exon
GCTGCGGGGAGAGCGTGCGGACGCCGCGTGTGCTGGGCGGGCGGCCGGCGGCCATCGAGGCCTGGCCATGGCAGGTCAGCCTGCGTTACCGCGGGGAGCACATCTGCGGCGGCAGCATCATCGATCCCCTCTGGATCCTCACTGCCGCGCACTGCTTCAG
Seq A exon
GTGAGCCGGGGCTGAAGTGTCCCCTAACGGTGCCGGCGCGACGCTGAGCAGCGCGTGGGCAGGGAGGGATGGGAGCAGTAACGTGTCCGTGCGCAG
Seq C2 exon
GAACAACCCCATCATCCCCAGCTGGCGCGTGAAGGCCGGCTCCGATGTCCTCTCTGGCCCTGCCAACCTTGCCGTGGAGAAGGTCTTCCTGGCCGAGGGGACGCCCACGTCTCCCAACAACAATGACATAGCGCTGGTGAAGCTACAGATCCCTCTGCATATCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007406:ENSGALT00000011978:6
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:
PF154941=SRCR_2=PD(5.4=9.3),PF0008921=Trypsin=PU(19.3=79.6)
A:
NA
C2:
PF0008921=Trypsin=FE(25.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCATCATCGATCCCCTCTGG
R:
ATTGTTGTTGGGAGACGTGGG
Band lengths:
171-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]