MmuINT0038675 @ mm9
Intron Retention
Gene
ENSMUSG00000020953 | Coch
Description
coagulation factor C homolog (Limulus polyphemus) [Source:MGI Symbol;Acc:MGI:1278313]
Coordinates
chr12:52703634-52704699:+
Coord C1 exon
chr12:52703634-52703860
Coord A exon
chr12:52703861-52704182
Coord C2 exon
chr12:52704183-52704699
Length
322 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TATTTTGTCTTTCCCATTAGGCT
3' ss Score
9.57
Exon sequences
Seq C1 exon
GAAAAGCCTTGAAGCACACTGCTCAGAAATTCTTTACAGCAGACACTGGTGTGAGAAAAGGAATACCAAAAGTGGTGGTAGTGTTTATTGATGGTTGGCCCTCTGATGACATTGAGGAAGCAGGCATTGTGGCCAGAGAGTTTGGTGTCAATGTATTTATAGTTTCTGTGGCCAAGCCCATTCCTGAAGAACTGGGGATGGTTCAAGATGTTGCATTTGTTGACAAG
Seq A exon
GTAAGGTGCAAGGGTTCTTGCTAGTGGGGAGGAGTGATTCATTTGGGGCCGACAAGCCCCTAACTAGATTAGTGAACATAAAATGTTTGATATGAGCCTAGAAGAATAAACCTGTAATCCTAGCTATTCAATGAGACCAAGACAACAGGTTCAGGGCCAGCCTATGCAATTAAGACCCCTAACTCAAAATGAAAAGTAACAAAGGCCTGGGAACACATGCATAAGGTTCTAGGTTCATTCTCCATTACTACATAATTTGCAAAATTTTGCGAGCTTTAAGCAACTTTTGATCTTTTGGGGTATATTTTGTCTTTCCCATTAG
Seq C2 exon
GCTGTGTGTCGGAATAATGGCTTCTTCTCTTATCACATGCCCAACTGGTTTGGCACTACAAAATATGTGAAGCCTCTGGTGCAGAAGCTCTGTACGCACGAACAGATGATGTGCAGCAAAACCTGCTACAACTCAGTGAACATTGCCTTTCTGATTGACGGCTCCAGCAGTGTTGGAGATAGCAATTTCCGCCTCATGCTAGAATTTGTTTCTAACATAGCGAAGACATTTGAAATCTCAGACATTGGAGCCAAGATAGCTGCTGTACAGTTCACTTATGACCAGCGCACCGAGTTCAGTTTCACTGACTATAATACCAAAGAGAACGTCCTAGCTGTCCTAGCGAACATCCGCTACATGAGTGGTGGCACAGCTACTGGTGATGCCATCGCCTTTACTGTTAGAAATGTATTTGGTCCCATAAGGGACAGCCCCAACAAAAACTTCCTGGTTATTGTCACAGATGGGCAGTCCTATGATGATGTCCGAGGCCCTGCTGCAGCTGCCCATGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020953-Coch:NM_007728:9
Average complexity
IR-S
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(46.3=100)
A:
NA
C2:
PF0009223=VWA=PD(3.1=2.9),PF0009223=VWA=PU(72.8=72.8)
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:
GCCCATTCCTGAAGAACTGGG
R:
GGTGCGCTGGTCATAAGTGAA
Band lengths:
343-665
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: