MmuINT0038951 @ mm10
Intron Retention
Gene
ENSMUSG00000032332 | Col12a1
Description
collagen, type XII, alpha 1 [Source:MGI Symbol;Acc:MGI:88448]
Coordinates
chr9:79678259-79678610:-
Coord C1 exon
chr9:79678461-79678610
Coord A exon
chr9:79678379-79678460
Coord C2 exon
chr9:79678259-79678378
Length
82 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGT
5' ss Score
7.03
3' ss Seq
GTCCATGCTGTTATTTTTAGCTC
3' ss Score
6.9
Exon sequences
Seq C1 exon
GGATGGATTGTCTCACCAGAGCTGAAGCAGACATTGTGTTGCTGGTGGATGGGTCATGGAGCATCGGCCGTGCAAATTTTAGAACTGTGCGAAGCTTCATTTCTCGTATTGTAGAAGTCTTTGAAATTGGCCCCAAAAGAGTACAAATTG
Seq A exon
GTAGGTTTCCTCAATACTGAAGACCTTTGATAACTTACTTGCTATCTTTTACACATCATAATGTCCATGCTGTTATTTTTAG
Seq C2 exon
CTCTCGCTCAGTACAGTGGAGACCCCAGAACAGAGTGGCAGTTAAATGCTCATAGAGACAAGAAGAGTTTATTACAGGCTGTGGCGAACTTACCATACAAAGGAGGAAATACCCTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032332:ENSMUST00000071750:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.049
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(23.1=78.4)
A:
NA
C2:
PF0009223=VWA=FE(23.1=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:
TCTCACCAGAGCTGAAGCAGA
R:
TCTGTTCTGGGGTCTCCACTG
Band lengths:
174-256
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