MmuINT0040356 @ mm10
Intron Retention
Gene
ENSMUSG00000004098 | Col5a3
Description
collagen, type V, alpha 3 [Source:MGI Symbol;Acc:MGI:1858212]
Coordinates
chr9:20773894-20774067:-
Coord C1 exon
chr9:20774014-20774067
Coord A exon
chr9:20773930-20774013
Coord C2 exon
chr9:20773894-20773929
Length
84 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TTCCCTGTCTCTTTCCACAGGGC
3' ss Score
13.93
Exon sequences
Seq C1 exon
GGTCTCCCTGGTCCTGTTGGCTCGTTAGGTCACCCTGGGCCCCCAGGTGTGGTG
Seq A exon
GTGAGTGTGGGGATATTGGAGGGATGGGGAAGTCATCATGATGGGTGGTATTGAGACCCCAACATTCCCTGTCTCTTTCCACAG
Seq C2 exon
GGCCCTCTGGGACAGAAGGGCTCCAAAGGGTCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004098:ENSMUST00000004201:60
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(20.0=100),PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(17.5=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:
GGTCTCCCTGGTCCTGTTGG
R:
GGACCCTTTGGAGCCCTTCT
Band lengths:
87-171
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