MmuINT0039834 @ mm10
Intron Retention
Gene
ENSMUSG00000026043 | Col3a1
Description
collagen, type III, alpha 1 [Source:MGI Symbol;Acc:MGI:88453]
Coordinates
chr1:45321497-45321992:+
Coord C1 exon
chr1:45321497-45321696
Coord A exon
chr1:45321697-45321941
Coord C2 exon
chr1:45321942-45321992
Length
245 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
ATATTCTTTATATGTTATAGGCT
3' ss Score
8.08
Exon sequences
Seq C1 exon
ATGAATTGGGATGCAGCCACCTTGGTCAGTCCTATGAGTCTAGAGATGTCTGGAAGCCAGAACCATGTCAAATATGTGTCTGTGACTCAGGATCTGTCCTTTGCGATGACATAATCTGTGATGAGGAGCCACTAGACTGCCCCAACCCAGAGATCCCATTTGGAGAATGTTGTGCAATATGCCCACAGCCTTCTACACCT
Seq A exon
GTGAGTCTGTAGAATATATAAACTCTTCAAAATCTACATCTTCAAGAACCATATTTAAACATGTAAATAGTCTCTACTGCATAGAGGTCTGAAAGAAATGCAAGCCATGTCTGTTGCCATGACAAGTGAATGGTGTCACTTTTAACAGAAAGCAGGAGATTGGGTATAATCAGATTTAAGAAATAAAGATGTAAATTGTGCTACAGTTTACATATATTAATCTCTATATTCTTTATATGTTATAG
Seq C2 exon
GCTCCTGTGCTTCCTGATGGCCATGGACCTCAAGGCCCCAAGGGAGATCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026043:ENSMUST00000087883:2
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=1.000
Domain overlap (PFAM):
C1:
PF0009313=VWC=WD(100=85.1)
A:
NA
C2:
PF0139113=Collagen=PU(24.5=70.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAATTGGGATGCAGCCACCTT
R:
GATCTCCCTTGGGGCCTTGAG
Band lengths:
247-492
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