MmuINT0038672 @ mm10
Intron Retention
Gene
ENSMUSG00000020953 | Coch
Description
cochlin [Source:MGI Symbol;Acc:MGI:1278313]
Coordinates
chr12:51598028-51598299:+
Coord C1 exon
chr12:51598028-51598072
Coord A exon
chr12:51598073-51598151
Coord C2 exon
chr12:51598152-51598299
Length
79 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CCTTCTCTGCCTCTCTGTAGACT
3' ss Score
10.98
Exon sequences
Seq C1 exon
GTAAAAGACTAAAGAAGACACCAGAGAAGAAGACTGGCAACAAAG
Seq A exon
GTAAGCTAATTGCTCGGGGAAATGGCAGGTCCTTGAGGTGCTCGGGGGACTAACGAAGCCCTTCTCTGCCTCTCTGTAG
Seq C2 exon
ACTGTAAGGCAGACATTGCATTTCTCATTGATGGAAGCTTCAATATTGGGCAGCGCCGATTTAATTTGCAGAAGAATTTTGTTGGGAAAGTGGCACTAATGTTGGGAATTGGAACAGAAGGACCACACGTGGGTCTCGTTCAAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020953:ENSMUST00000164782:6
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(27.8=90.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGAGAAGAAGACTGGCAAC
R:
CTTGAACGAGACCCACGTGTG
Band lengths:
169-248
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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