MmuALTA1007883-2/2 @ mm10
Alternative 3'ss
Gene
ENSMUSG00000020953 | Coch
Description
cochlin [Source:MGI Symbol;Acc:MGI:1278313]
Coordinates
chr12:51596444-51597077:+
Coord C1 exon
chr12:51596444-51596577
Coord A exon
chr12:51597015-51597017
Coord C2 exon
chr12:51597018-51597077
Length
3 bp
Sequences
Splice sites
5' ss Seq
CCAGTAGGT
5' ss Score
5.41
3' ss Seq
TTAACTTCTCATTTCTACAGAAG
3' ss Score
8.84
Exon sequences
Seq C1 exon
GGGAGTGATTGGCACCTCAGGGGGACCTGTGCGTGTCTACAGCCTTCCTGGTCGAGAGAACTACTCCTCGGTAGATGCCAACGGCATCCAGTCTCAGATGCTTTCCCGATGGTCCGCGTCCTTCGCTGTGACCA
Seq A exon
AAG
Seq C2 exon
GCAAAAGCAGTACCCAGGAAGCCACAGGACGGGCAGTGTCCACAGCCCACCCACCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020953-8-8,8-7-2/2
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 Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTCCTCGGTAGATGCCAACG
R:
GGCTTCCTGGGTACTGCTTTT
Band lengths:
95-98
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types