GgaINT0054591 @ galGal4
Intron Retention
Gene
ENSGALG00000009920 | Protein
Description
Cochlin [Source:UniProtKB/Swiss-Prot;Acc:O42163]
Coordinates
chr5:33530126-33530402:+
Coord C1 exon
chr5:33530126-33530170
Coord A exon
chr5:33530171-33530254
Coord C2 exon
chr5:33530255-33530402
Length
84 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
ATTATTTTGAATGCTCGCAGACT
3' ss Score
6.14
Exon sequences
Seq C1 exon
GCAAAAGACCTAAGAAGACCCTCGAGAAAAAGGCTGGAAACAAAG
Seq A exon
GTAGGAATTCACTGGTTTAACTTTTGAAAAACAAAACCCTAACATGTATTTGGTGCTAAGTCTAATTATTTTGAATGCTCGCAG
Seq C2 exon
ACTGTAAAGCTGATATTGCATTTCTCATTGATGGAAGTTACAACATCGGCCAACGTAGATTTAATCTGCAGAAAAACTTTGTTGGAAAAGTAGCGGTAATGTTGGGAATTGGAACGGAAGGGCCTCATGTTGGAGTTGTACAAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009920:ENSGALT00000016132:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(26.9=90.0)
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:
GACCCTCGAGAAAAAGGCTGG
R:
CAACTCCAACATGAGGCCCTT
Band lengths:
167-251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]