MmuINT0040706 @ mm10
Intron Retention
Gene
ENSMUSG00000027570 | Col9a3
Description
collagen, type IX, alpha 3 [Source:MGI Symbol;Acc:MGI:894686]
Coordinates
chr2:180611429-180612989:+
Coord C1 exon
chr2:180611429-180611500
Coord A exon
chr2:180611501-180612953
Coord C2 exon
chr2:180612954-180612989
Length
1453 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
AGAACCTTCTCTCTGCCTAGGGT
3' ss Score
8.2
Exon sequences
Seq C1 exon
GGACAAAAAGGCAGCACAGGAGACCCTGGCCTTCCGGGCCCCCAAGGCCTACGGGGAGATGTGGGTGACCGG
Seq A exon
GTAAGGGTTGTTCTCTTGCACCTCCCTGCTCTAACCAGTCTACATAGACTCAAGCCAGCAGCAGCCCACTCCTTCCCACGTGGGTGGCAGGGATGGCAGCACCAACTATGTGGACAGGTACCCTTGATTCTTTTCTTGCTCATTCTCTTGGTGTTCTTGGGCAAGAAGGGATCTAGGGTCCTTACTGCTCTATCACAAGCCCTGCATGCAGGCCTAGAAGAATCAGTAACTGGGGTGAGGGGAGAAGTGTAAACTTGAGACTCTAGGTCCTGGGCTGCATGCAGTTTGGTGTGAGCTCAGACCTGAATGACCCCAGTGTTTCAAACATGTAACTTTCCAAGAGTCTTTGCTGATGGTGCTGCAGTAGCCAGTGGCATTGGTGTTCTGCAGGGACAGGATCCAGGGAGTTATGACTTACTCAGGTTCTCAATGGTTAATAGATAATGCCTGGGTCCCCTGGAAGGAGTCTGGGGGTCTGGTCTGGGTCTAGACCATACATCAGATCTTTACAGGCTATGTGACTGCTTTCTTGATCTCCACTTGGCAAGGACAAAGCACTCTTTAAATGTGTGCATGCAATCATTGGAGGCTCTAGGGTACCTGTGCAGACACAGGGAGCCACAGAAACCAGCACCACACAGCAGGGACAGTGGGTGCTTTATTAGCCTCTAGGCAGGAAATTCCAGGGGTTAGGGAATTTGCCAATAGCTCTGAGGACTCTAAGCTAGTGGAGGGAAATGCTTGCGCTGAGCCCCAGTCCCAGCAGGGAGGACGCTTTACTGACTTTCTCTTTGGATAGCTCTTGCCTTCACTTTCACATTTACTTCTCTTTTTAAAAAAGATTTATTTATTTTAATCTTATGTATAAACTTGCCCACATGGATGCATGTGTACCATATCTATCAAGAGCCAAAGGATGTCAGAGGGAATGTCAGTCAGTCCCTGGAACTAGAGTTACAGATGGATGTGAGCCACTTGATGCAATGCTGGGAACCAAACCCAGGTTCTCTACAAGAGCAGTGCTCGATCTATGTCTCTCTCTCTGTCTCTCTGTCTCTGTCTGTCTGTCTGTCTCTCTCTCTCTCTCTCTCTCTCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAATGAGTAAATGAGTGTGTATGACAGAGAGGGGGCAGGGAGAGAGATCCAAGACAGCAGTAGCCGATCTATTCGATGTCCACTGAGTGATAGGCAGCTGCTCTTGAAAGGACCAGTAGGGCATGCATGGCTGTATACTACTGTTATCTATGGACTTGGGTTTGGCAACTGGGGCTAGGGTGCTGTTTCTAAGACCCCTTCCATAGGAGGAATTTCTATACCTACTGTAGGTGGAATTCCTGCCTCTGCTATGCAGGGCCATGACCCTCCCCCCATGGGGATTCCCAGGGTTCCTCTAATCCAGAACCTTCTCTCTGCCTAG
Seq C2 exon
GGTCCAGGAGGTGCCACAGGCCCTAAGGGAGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027570:ENSMUST00000132527:25
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=PU(31.5=95.8)
A:
NA
C2:
PF0139113=Collagen=FE(15.1=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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