MmuINT0040327 @ mm10
Intron Retention
Gene
ENSMUSG00000004098 | Col5a3
Description
collagen, type V, alpha 3 [Source:MGI Symbol;Acc:MGI:1858212]
Coordinates
chr9:20787090-20787314:-
Coord C1 exon
chr9:20787261-20787314
Coord A exon
chr9:20787135-20787260
Coord C2 exon
chr9:20787090-20787134
Length
126 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
GCTCATTTCATATGTTCTAGGGT
3' ss Score
8.34
Exon sequences
Seq C1 exon
GGCACCCGAGGAGACAGGGGACAGCCGGGGGCCACAGGCCAGCCTGGCCCCAAG
Seq A exon
GTATGGGAGTGAGTAGCGATTGGGGGATGACCAAGGGTCCTTGTCTATCTCAGGCTAACTTAGCTACCTGCTTAGTTCTTCCAGTTGAGTATGTTCTGGTATTGAAGCTCATTTCATATGTTCTAG
Seq C2 exon
GGTGACGTGGGCCAGAATGGGTCTCCTGGGCCCCCTGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004098:ENSMUST00000004201:34
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(18.3=100),PF0139113=Collagen=PU(9.2=44.4)
A:
NA
C2:
PF0139113=Collagen=FE(15.1=100),PF0139113=Collagen=FE(16.1=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:
GGCACCCGAGGAGACAGG
R:
CTTTTCTCCAGGGGGCCCAG
Band lengths:
99-225
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