MmuINT1007494 @ mm10
Intron Retention
Gene
ENSMUSG00000048126 | Col6a3
Description
collagen, type VI, alpha 3 [Source:MGI Symbol;Acc:MGI:88461]
Coordinates
chr1:90785722-90785940:-
Coord C1 exon
chr1:90785890-90785940
Coord A exon
chr1:90785758-90785889
Coord C2 exon
chr1:90785722-90785757
Length
132 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGT
5' ss Score
6.93
3' ss Seq
GTGTTTGTTGTCTTTTACAGGGA
3' ss Score
12.76
Exon sequences
Seq C1 exon
GGAGATGACGGGAGAGATGGGGTTGGCAGTGAAGGACGCAGAGGCAAAAAA
Seq A exon
GTATGTATCTGTTGAAGCTTCTAGAGACGCCCTCATTGTTGAGAGTCACCAAGGATGGCTTCTGACATCTTGTATTAGAATTGATGGCTTTAAGTTGGGACCTGATACTGAGGTGTTTGTTGTCTTTTACAG
Seq C2 exon
GGAGAAAGAGGCTTCCCTGGGTATCCGGGACCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000048126:ENSMUST00000097653:26
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:
NO
A:
NA
C2:
PF0139113=Collagen=PU(12.7=66.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGACGGGAGAGATGGGGTT
R:
CTTTGGTCCCGGATACCCAGG
Band lengths:
84-216
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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