MmuINT0039838 @ mm10
Intron Retention
Gene
ENSMUSG00000026043 | Col3a1
Description
collagen, type III, alpha 1 [Source:MGI Symbol;Acc:MGI:88453]
Coordinates
chr1:45334007-45334312:+
Coord C1 exon
chr1:45334007-45334060
Coord A exon
chr1:45334061-45334213
Coord C2 exon
chr1:45334214-45334312
Length
153 bp
Sequences
Splice sites
5' ss Seq
CCTGTATGT
5' ss Score
4.27
3' ss Seq
GCAAGTGTTTTTCTTACTAGGGA
3' ss Score
6.21
Exon sequences
Seq C1 exon
GGTATGCCCGGAAGTCCAGGTGGACCAGGCAATGATGGAAAACCAGGACCTCCT
Seq A exon
GTATGTACAATTATGATGTCTTGTTTTACTAACCCAGTAAAAAAAAATGAAATGCATACATTGGATAGATTTGAGTGTGTGTATATGTATGTGTATTATAATTAGATTATTTGTTCATCAAGTCCTGATTATGGCAAGTGTTTTTCTTACTAG
Seq C2 exon
GGAAGTCAAGGAGAAAGTGGTCGCCCTGGTCCCCCTGGCCCATCTGGTCCCAGAGGTCAGCCTGGTGTCATGGGTTTCCCTGGTCCTAAAGGAAATGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026043:ENSMUST00000087883:23
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(28.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(53.3=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:
GTATGCCCGGAAGTCCAGGT
R:
TCCTTTAGGACCAGGGAAACCC
Band lengths:
146-299
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