MmuINT0039849 @ mm10
Intron Retention
Gene
ENSMUSG00000026043 | Col3a1
Description
collagen, type III, alpha 1 [Source:MGI Symbol;Acc:MGI:88453]
Coordinates
chr1:45338574-45338763:+
Coord C1 exon
chr1:45338574-45338627
Coord A exon
chr1:45338628-45338709
Coord C2 exon
chr1:45338710-45338763
Length
82 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACA
5' ss Score
8.92
3' ss Seq
ATCATTTGATCTTTTCTCAGGGT
3' ss Score
7.99
Exon sequences
Seq C1 exon
GGTCCTGCTGGCCCTATTGGTCCCCCTGGCCCAGCTGGTCAGCCTGGAGATAAG
Seq A exon
GTAACAAAACTACTGGAAACAAAAATCAATCTTTGCTTTAATAGACATAGAACAGTAACAATATCATTTGATCTTTTCTCAG
Seq C2 exon
GGTGAAGGTGGTTCCCCTGGACTTCCAGGTATAGCTGGACCTCGAGGTGGCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026043:ENSMUST00000087883:33
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(21.8=100),PF0139113=Collagen=PU(3.0=11.1)
A:
NA
C2:
PF0139113=Collagen=PD(22.9=84.2),PF0139113=Collagen=FE(30.0=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:
TCCTGCTGGCCCTATTGGTC
R:
CCTCGAGGTCCAGCTATACCTG
Band lengths:
99-181
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