MmuINT0038674 @ mm10
Intron Retention
Gene
ENSMUSG00000020953 | Coch
Description
cochlin [Source:MGI Symbol;Acc:MGI:1278313]
Coordinates
chr12:51601814-51602873:+
Coord C1 exon
chr12:51601814-51601917
Coord A exon
chr12:51601918-51602646
Coord C2 exon
chr12:51602647-51602873
Length
729 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
GCTCATTTGCTTGTTTTTAGGAA
3' ss Score
9.05
Exon sequences
Seq C1 exon
TGAACACCCCAAAATAGAATTTTACTTGAAAAACTTTACTTCAGCCAAAGATGTCTTGTTTGCCATAAAAGAAGTAGGTTTCCGAGGGGGTAACTCCAACACAG
Seq A exon
GTAAGCACACAGATGCTTAGAGATTAGACCTGAAAGCCGCATGCTTCATGACATTCATGACAGTTCTAGCACTTCAGTTTTGGCAGGATCTGCATATCAGCATCTGACACCTCTCTATAATGGAAAATATTCCAATGGGTTAGCTGATTTTTCTTTTTGGTTTTTTGGAGACAAGATTTTTCTATGTAGCCCTGGCTATCCTGGAACTGTATACCAGACTGGCCTCAAACTCAAGAGATTGGCATGCCTCTGCCTCCCAAGTGGTGGCATTAAAGATGTGCATCACCATGGCTGGTGCTAATAATTCTTAAAAACAAAACAAAAACTCTACATCATTCTGAATTTATAATCCTTACATTAGATAGGTCATTTACTTCTTTAGGAAAGTACCTATTTATAATCCAAAAAATCAACAATGAAGGAAGATGGGGCAGACTTTGGAAGGCTCCTTGTTCCCTAGCTGTCCTCATAGGTCAGGAAGGGTAAGGGTACATGACAGAAGTGGGTGTGGCTTGTTTGTTGGTATTGTTAACTGAAGGAAATGTGAGACTTCTGGAAGGTGGAGGGGAAGCATTGTGGGTTGTGAAGGCCAAAACTAGGTCTGAAGAAGAATAATAATATTTTTGCTAACTGAATTCCATGAGTTAAATTCTTAATGGCATCGTTATTAACCTGAAATAGAAATATAATCTGAGCCACTACAAATGATGCTCATTTGCTTGTTTTTAG
Seq C2 exon
GAAAAGCCTTGAAGCACACTGCTCAGAAATTCTTTACAGCAGACACTGGTGTGAGAAAAGGAATACCAAAAGTGGTGGTAGTGTTTATTGATGGTTGGCCCTCTGATGACATTGAGGAAGCAGGCATTGTGGCCAGAGAGTTTGGTGTCAATGTATTTATAGTTTCTGTGGCCAAGCCCATTCCTGAAGAACTGGGGATGGTTCAAGATGTTGCATTTGTTGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020953:ENSMUST00000164782:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(21.6=100)
A:
NA
C2:
PF0009223=VWA=FE(46.3=100)
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:
TGAACACCCCAAAATAGAATTTTACT
R:
TCAACAAATGCAACATCTTGAACCA
Band lengths:
327-1056
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