MmuINT0040690 @ mm9
Intron Retention
Gene
ENSMUSG00000027570 | Col9a3
Description
collagen, type IX, alpha 3 [Source:MGI Symbol;Acc:MGI:894686]
Coordinates
chr2:180332927-180333639:+
Coord C1 exon
chr2:180332927-180333030
Coord A exon
chr2:180333031-180333570
Coord C2 exon
chr2:180333571-180333639
Length
540 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ATAACTTATCTCAATTTCAGAAA
3' ss Score
8.89
Exon sequences
Seq C1 exon
CGTCGCTCGGCGCCTGCCGCTCAGAGCGCCTGCCAGCCATGACCGGAGCGCCTGCCCTAGCCCTGCTGCTGCTGGGGCAGCTCCTGACGGCCACCTCCGCGCAG
Seq A exon
GTGAGCGCGGGCCCGCGGGTGCTTATGGGGTCGGGGATAGGGCCGGACGTCGAACCGAACAGCCTGGGACAACTCGAGTCCCTTGGGCCAACACCTGAGTCCCGCCGCCAAGGACCCTCGAGGACATCTGTGGCAGTCTCTTCACCGCCTCTCCGGCTGGCGAGTTCTGGTGATGCAGCTGAGCTCCACGGACACCAGGACATGTCAACCATGATCCTAGGCTTCCATTTGTCTTCACCCAACCGGGTCAGGCCGCTGCCAAGCGCTGCCACCACTGCCACCAAGCTCTGAACACACAATGTTGCCTTTGTTCCTGGAGACTCCCTGCGGGGCCGCAGCACAGCCACTCCTGGCGCAAAGGAGGATAAACTGCCTTGGCGCCAGGCTCCAGCGCAGGAGACTGGGGTTTTTTAAGGCAGGCAGGGAGGAGGATTATGGGCCACTGTCACAGGACCCAGAGTTTCTTGGGCTGGGGAAGATGGGACGGAAGGGCTGACATGTTGGAAAAGAAGCCTACCTAATAACTTATCTCAATTTCAG
Seq C2 exon
AAAGTGGGACCCCGAGGCCCCCCTGGTCCCCAAGGGCCTCCTGGAAAACCCGGCAAGGATGGCATTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027570-Col9a3:NM_009936:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.889 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(1.7=4.5)
A:
NA
C2:
PF0139113=Collagen=FE(36.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: