GgaALTA0005236-2/2 @ galGal4
Alternative 3'ss
Gene
ENSGALG00000009920 | Protein
Description
Cochlin [Source:UniProtKB/Swiss-Prot;Acc:O42163]
Coordinates
chr5:33528732-33529251:+
Coord C1 exon
chr5:33528732-33528865
Coord A exon
chr5:33529186-33529188
Coord C2 exon
chr5:33529189-33529251
Length
3 bp
Sequences
Splice sites
5' ss Seq
CTCGTAGGT
5' ss Score
4.63
3' ss Seq
TCGTTCTTCCAATATTTTAGCAG
3' ss Score
6.06
Exon sequences
Seq C1 exon
AGGGGTGATCACCAACGCAGGAGGAGCTGTAAGAGTACAGACTCTCCCAGGACAGGAAAACTACCCGGCTGTACATGCCAATGGGATCCAGTCTCAGGTGCTCTCTAGATGGGCTTCATCTTTCTCAGTGACTC
Seq A exon
CAG
Seq C2 exon
GTACCAACAACCTAGCGCTTGAAGCAGTGGGACGATCAGTTGCAACAGCACGACCTGCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009920-9-7,9-6-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.217
Domain overlap (PFAM):
C1:
PF0381514=LCCL=PD(45.6=89.1)
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATCCAGTCTCAGGTGCTCT
R:
GTTGCAACTGATCGTCCCACT
Band lengths:
97-100
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]