MmuINT0040710 @ mm10
Intron Retention
Gene
ENSMUSG00000027570 | Col9a3
Description
collagen, type IX, alpha 3 [Source:MGI Symbol;Acc:MGI:894686]
Coordinates
chr2:180615477-180615857:+
Coord C1 exon
chr2:180615477-180615623
Coord A exon
chr2:180615624-180615802
Coord C2 exon
chr2:180615803-180615857
Length
179 bp
Sequences
Splice sites
5' ss Seq
CCGGTGCGT
5' ss Score
9.74
3' ss Seq
TGAACCTGGGTGAATTTCAGGGC
3' ss Score
5.81
Exon sequences
Seq C1 exon
TCTGGCAGCCGAGGGGAACTGGGCCCCAAAGGCATCCAGGGCCCCAATGGCACCAGTGGAGTCCAGGGTGTACCTGGTCCCCCAGGTCCACTGGGCCTCCAAGGTGTGCAGGGTGTCCCAGGCATCACCGGGAAGCCTGGAGTTCCG
Seq A exon
GTGCGTAGCTTTTTCTTTCTCTTGTGTTGTGGGTTTTGGACTTGTGCTAGACTTAGATCATGTTTGGGTGTTGTTTTTGTTATGTAGTGAACTATCAGTTGTTTTGGGAGTGAGGTACTAGGTAGGTCAGAACTACTGGTGCACTGCCTCACCTGCTGATGAACCTGGGTGAATTTCAG
Seq C2 exon
GGCAAGGAAGCCAGTGAACAGCGCATCAGGGAGCTATGCGGGGGTATGATCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027570:ENSMUST00000132527:29
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=PD(13.7=20.4),PF0139113=Collagen=FE(76.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(7.9=26.3)
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:
CAGCCGAGGGGAACTGGG
R:
TGATCATACCCCCGCATAGCT
Band lengths:
194-373
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