MmuINT0040347 @ mm9
Intron Retention
Gene
ENSMUSG00000004098 | Col5a3
Description
collagen, type V, alpha 3 [Source:MGI Symbol;Acc:MGI:1858212]
Coordinates
chr9:20580536-20580810:-
Coord C1 exon
chr9:20580757-20580810
Coord A exon
chr9:20580590-20580756
Coord C2 exon
chr9:20580536-20580589
Length
167 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CCACTGTCTCTCCTCCCTAGGGT
3' ss Score
12.4
Exon sequences
Seq C1 exon
GGTCCCACAGGACTCCCTGGAGATCTAGGGCCCCCAGGAGACCCTGGAGTTCCG
Seq A exon
GTGAGTGTAAATGCTCCCTGTAGCCTAGCCCTAAATATATCAATGTATCTGCATTTACCCCCATGCCCCTATCCTTGACCCGCTTAGAGGAGTGTATGGCCCTCACTCTCCTCCAGCTCCATCTCTATCCCAACTATCCCAAGACTCCCACTGTCTCTCCTCCCTAG
Seq C2 exon
GGTATTGATGGCATCCCAGGGGAGAAGGGAAATGCTGGTGATATTGGGGGACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004098-Col5a3:NM_016919:52
Average complexity
IR-S
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(17.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.3=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:
AGGACTCCCTGGAGATCTAGG
R:
GGTCCCCCAATATCACCAGCA
Band lengths:
99-266
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: