MmuINT0039366 @ mm9
Intron Retention
Gene
ENSMUSG00000001506 | Col1a1
Description
collagen, type I, alpha 1 [Source:MGI Symbol;Acc:MGI:88467]
Coordinates
chr11:94806066-94806281:+
Coord C1 exon
chr11:94806066-94806119
Coord A exon
chr11:94806120-94806227
Coord C2 exon
chr11:94806228-94806281
Length
108 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CTCCACCTCCCACCTTACAGGGT
3' ss Score
8.39
Exon sequences
Seq C1 exon
GGTCCTGCTGGTGAGAGAGGTGAACAAGGTCCCGCTGGCTCCCCTGGATTCCAG
Seq A exon
GTGAGGCTTCATGACTTAGGTTTGCAGGGAAGAGTGCAGAACACTCCTTTGTTAACTGTTAAAGATTCTAAATCCTACCTCTTCTCCCCTCCACCTCCCACCTTACAG
Seq C2 exon
GGTCTTCCTGGTCCTGCCGGTCCTCCTGGTGAAGCAGGCAAGCCTGGTGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001506-Col1a1:NM_007742:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(18.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(11.8=61.1)
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:
GTCCTGCTGGTGAGAGAGGT
R:
CTGTTCACCAGGCTTGCCTG
Band lengths:
107-215
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: