MmuINT0039352 @ mm10
Intron Retention
Gene
ENSMUSG00000001506 | Col1a1
Description
collagen, type I, alpha 1 [Source:MGI Symbol;Acc:MGI:88467]
Coordinates
chr11:94941547-94941781:+
Coord C1 exon
chr11:94941547-94941591
Coord A exon
chr11:94941592-94941727
Coord C2 exon
chr11:94941728-94941781
Length
136 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
AACTTCCATTTCATCCACAGGGT
3' ss Score
9.05
Exon sequences
Seq C1 exon
GGTGCTCGCGGTAACGATGGTGCTGTTGGTGCTGCTGGACCCCCT
Seq A exon
GTAAGTATGGCCTTGACTTTGAGTATGGGAGTAGGGTGAGACCTCAGGGTCAGCTCTTGGGGCTGACATCAACTTTTGAAACTTAGAAGCTCTTAGTCTCCTCCACCTTGTAGCTAAACTTCCATTTCATCCACAG
Seq C2 exon
GGTCCCACCGGCCCCACTGGCCCTCCTGGCTTCCCTGGTGCAGTTGGTGCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001506:ENSMUST00000001547:15
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(23.3=100),PF0139113=Collagen=PU(5.7=33.3)
A:
NA
C2:
PF0139113=Collagen=FE(28.3=100),PF0139113=Collagen=FE(19.5=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:
GGTAACGATGGTGCTGTTGGT
R:
CACCAACTGCACCAGGGAAG
Band lengths:
85-221
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