MmuINT0173998 @ mm10
Intron Retention
Gene
ENSMUSG00000048832 | Vps37c
Description
vacuolar protein sorting 37C [Source:MGI Symbol;Acc:MGI:2147661]
Coordinates
chr19:10710270-10711353:+
Coord C1 exon
chr19:10710270-10710441
Coord A exon
chr19:10710442-10711270
Coord C2 exon
chr19:10711271-10711353
Length
829 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGG
5' ss Score
4.66
3' ss Seq
CTCTCTGCCCTTCCTTCCAGAGA
3' ss Score
11.55
Exon sequences
Seq C1 exon
GTTCAGGACCTGCAGTTAGAACGAGAGATGGCACTGGCCACGAACCGGAGCCTGGCAGAGCAGAACCTGGAGTTCCAAGGTCCCCTGGAAATCAGCCGCTCTAACCTCTCAGACAAATACCAGGAGCTGCGGAAGCTTGTGGAGCGGTGCCAGGAGCAGAAAGCCAAGCTGG
Seq A exon
GTAGGGACAGCCGACCACAGACAAGCACTCTGGCCATCTCCCCTGCTGATTGATACTTCTGTTCAAAGGAGGACGAGGGAGGCAGCTGGAATACTAAGGATGCTTAGATACCCAGAATCGGAGAGGGCCAGCAGCCATTGTAGCCACTGTGCTTTGCATGTTTTTACATGATAATAAGCAAATAAGCAAAAGTGTAGGTACTGTAGTTAGTCTAAATGTTTGAGTATTTATATTTATTGTATACCCTGGTGATAATTTTCATAGTATTAAAAATGTCCTGAACTTACTATTTTTATAGATGAGGAAAACAAGGCTGGAGCCGGCCGAGGGCTTGCCTGAGGTCATCCCACCAGAGTGAGATGGAGTTGGGATTTGCAAGCATAGCCTTTAAGAGCTGAGCATCTCTCTAGCCCTGGAATGGGATTTGAATCTAGGCAGTCAGTATGTTTCACTGCCTCTGCCAACTTAGCCCCGAGCCTTGCAGAGCTGACCTAGGCCCTGTGAGGTAGGAAGGCTTCCTGGATGGCTGTGCCCTTGGCAGCTGCTTGGCCAAGACCTGAGCTTGTCCCTCAGCTCCTCTTCACCAAGATGGTGAACGCCTACATGAACCAAAAGGACCCCACAGAACCAGCTGCAGGGACTCTCTCTCCACTGGGGCCTGTTGTGGCTGAGTCCTGAGTGCTCACAGAACCAGCAGCAGGGACTCTATCTATAGTGGCTAGGCCCAAGCACACAAAGGGCATGTCACATGTCTTCCCTGAAATCAGGGTCCTCAGCTTTAATTAAAGCAGTGCTTTTGAAATGTCGACCTCTCTGCCCTTCCTTCCAG
Seq C2 exon
AGAAATTTTCCTCGGCACTGCAGCCTGGGACCTTGTTGGACCTTCTGCAGATCGAAGGCATGAAGATCGAGGAGGAGTCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000048832:ENSMUST00000087951:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.138 A=NA C2=0.286
Domain overlap (PFAM):
C1:
PF072008=Mod_r=FE(38.0=100)
A:
NA
C2:
PF072008=Mod_r=FE(18.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCAGGACCTGCAGTTAGAACG
R:
CTCAGACTCCTCCTCGATCTTCA
Band lengths:
254-1083
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