MmuINT0039355 @ mm10
Intron Retention
Gene
ENSMUSG00000001506 | Col1a1
Description
collagen, type I, alpha 1 [Source:MGI Symbol;Acc:MGI:88467]
Coordinates
chr11:94942204-94942440:+
Coord C1 exon
chr11:94942204-94942248
Coord A exon
chr11:94942249-94942341
Coord C2 exon
chr11:94942342-94942440
Length
93 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
GTCTGTCCTGACTCCTGCAGGGT
3' ss Score
9.34
Exon sequences
Seq C1 exon
GGAAACCCTGGTGCTGATGGACAACCTGGCGCTAAAGGTGCCAAT
Seq A exon
GTAAGTCTCTAGCAGCCCTCCTCCCATGAGCCACCTGCCACCTGCCCCATGCCCTCCACCCTTGGGCTAAAATGTCTGTCCTGACTCCTGCAG
Seq C2 exon
GGTGCTCCTGGTATTGCTGGTGCTCCTGGCTTCCCTGGTGCCCGAGGCCCCTCTGGACCCCAGGGCCCCAGCGGCCCTCCAGGTCCCAAGGGTAACAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001506:ENSMUST00000001547:18
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:
PF0139113=Collagen=FE(16.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(16.1=42.4)
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:
GAAACCCTGGTGCTGATGGAC
R:
ACTGTTACCCTTGGGACCTGG
Band lengths:
143-236
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