MmuINT0040711 @ mm9
Intron Retention
Gene
ENSMUSG00000027570 | Col9a3
Description
collagen, type IX, alpha 3 [Source:MGI Symbol;Acc:MGI:894686]
Coordinates
chr2:180350508-180351268:+
Coord C1 exon
chr2:180350508-180350562
Coord A exon
chr2:180350563-180351085
Coord C2 exon
chr2:180351086-180351268
Length
523 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
GACACTCTGTTTTCCAAAAGAGC
3' ss Score
4.29
Exon sequences
Seq C1 exon
GGCAAGGAAGCCAGTGAACAGCGCATCAGGGAGCTATGCGGGGGTATGATCAGTG
Seq A exon
GTGAGTCTCCTGTGCATACCCTGCCTTTCACACAGCTCTGACCTTCTGTTATCCCTACCTTACCTGTCCTCTGATCTCCAGGAGGGCTACCCTCTCCCCAGCGCTTGATACAGTGCAGGGTACTCAGAGGAGCTCTGACTAACTACTGAGGGTAACAATTACAAGGAAGAACCCGGGTGGTGGTGGTGCATGCCTTTAATCCCTGTACTTGAGAGGTGCATCCTGGAGTTTGAGGACAGCCTGATCTACAGAGTGAGTTCCAGGACAGGAAGAAACCACTGTGCCCTTTGGCTAGAAGGGACACTTTCTTGAATAGCTTTGAACTTCTCATTCCAGCATGTGAGATAGTCCAAGAGAAGGGACCCTCCTGTCTCCCCTGGCATACTCTAGAGCAGATAAAGTAATCATTTTTGGTCAGTAAATGAAATCCCCTTCTGACAGAGAGCTGGCTTTGTTATACTTTGCATGAAGATGTTTGGTAATCCTCTCTGAAGTATGCACTTGACACTCTGTTTTCCAAAAG
Seq C2 exon
AGCAAATTGCACAGTTGGCTGCACACCTGAGGAAGCCCTTAGCACCAGGCTCCATCGGCAGGCCTGGTCCAGCTGGCCCCCCAGGCCCTCCAGGCCCTCCAGGCTCTATTGGCCACCCTGGCGCTCGGGGTCCCCCTGGATACCGTGGTCCCACTGGGGAACTAGGAGATCCTGGACCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027570-Col9a3:NM_009936:29
Average complexity
IR-S
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(7.9=26.3)
A:
NA
C2:
PF0139113=Collagen=PU(75.8=75.8)
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:
CAAGGAAGCCAGTGAACAGCG
R:
GTCCAGGATCTCCTAGTTCCCC
Band lengths:
230-753
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: