MmuINT0040699 @ mm10
Intron Retention
Gene
ENSMUSG00000027570 | Col9a3
Description
collagen, type IX, alpha 3 [Source:MGI Symbol;Acc:MGI:894686]
Coordinates
chr2:180609326-180609534:+
Coord C1 exon
chr2:180609326-180609379
Coord A exon
chr2:180609380-180609480
Coord C2 exon
chr2:180609481-180609534
Length
101 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGT
5' ss Score
8.46
3' ss Seq
CCTACTCACTGTCCTTACAGGGA
3' ss Score
9.99
Exon sequences
Seq C1 exon
GGCATGCCAGGCAAGGATGGCAAAGATGGTGTGCCGGGACTTGATGGTGAGAAG
Seq A exon
GTTGGTGTCCGGCTGGATGCTTGCTGGGAGGAGGTGGAGGAGTTCAGCTTCCCAAGGCCTCAGCATCATCTGGCCTCATACCCTACTCACTGTCCTTACAG
Seq C2 exon
GGAGAGGCTGGTCGCAATGGTGGCCAAGGAGAGAAAGGCCCCAATGGGCTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027570:ENSMUST00000132527:19
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(16.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(4.7=27.8)
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:
GCATGCCAGGCAAGGATGG
R:
CCATTGGGGCCTTTCTCTCCT
Band lengths:
100-201
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