MmuINT0039364 @ mm10
Intron Retention
Gene
ENSMUSG00000001506 | Col1a1
Description
collagen, type I, alpha 1 [Source:MGI Symbol;Acc:MGI:88467]
Coordinates
chr11:94944355-94944651:+
Coord C1 exon
chr11:94944355-94944408
Coord A exon
chr11:94944409-94944597
Coord C2 exon
chr11:94944598-94944651
Length
189 bp
Sequences
Splice sites
5' ss Seq
GTTGTAAGT
5' ss Score
8.3
3' ss Seq
TTATTGCCTTCTCCCCACAGGGT
3' ss Score
12.71
Exon sequences
Seq C1 exon
GGAGAACCTGGAAAGGCTGGAGAGCGAGGCCTTCCCGGACCCCCTGGCGCTGTT
Seq A exon
GTAAGTATCTCTTTGGAGTCTCTGACCTTTCTGCCCCTGCCTGTGACATACACCATCCTCCCATGGAGGATGTCTGCAGCCACTGTCACAACATCGGAAGTCACTAGGGGGCTCTGCTGTGTCTCAGAGGTCCAGTCCCTACCTGCGGCTCTCATCTCCCATACTGAATTTATTGCCTTCTCCCCACAG
Seq C2 exon
GGTCCTGCTGGCAAAGATGGAGAAGCTGGAGCTCAGGGAGCCCCTGGCCCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001506:ENSMUST00000001547:26
Average complexity
IR
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=FE(18.3=100)
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:
AGAACCTGGAAAGGCTGGAGA
R:
TCCAGCTTCTCCATCTTTGCC
Band lengths:
82-271
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