RnoALTA0009666-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000005286 | Coch
Description
cochlin [Source:RGD Symbol;Acc:1308536]
Coordinates
chr6:72363061-72363731:+
Coord C1 exon
chr6:72363061-72363194
Coord A exon
chr6:72363669-72363671
Coord C2 exon
chr6:72363672-72363731
Length
3 bp
Sequences
Splice sites
5' ss Seq
CCAGTAGGT
5' ss Score
5.41
3' ss Seq
TAAACTTCTCATTTCGACAGAAG
3' ss Score
5.95
Exon sequences
Seq C1 exon
GGGAGTGATTGGCACCTCAGGGGGCCCAGTGCGTGTCTATAGCCTTCCTGGTAGAGAGAACTATTCCTCGGTGGCTGCCAATGGCATTCAGTCTCAGACCCTTTCCAGATGGTCTGCTTCCTTCGCTGTGACCA
Seq A exon
AAG
Seq C2 exon
GCAAAAGCAGTACCCAGGAAGCCACGGGACGGGCAGTGTCCACAGCCAATCCGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005286-6-5,6-4-2/2
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=0.682
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
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACTATTCCTCGGTGGCTGC
R:
GGCTTCCTGGGTACTGCTTTT
Band lengths:
100-103
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]