MmuINT0039405 @ mm10
Intron Retention
Gene
ENSMUSG00000029661 | Col1a2
Description
collagen, type I, alpha 2 [Source:MGI Symbol;Acc:MGI:88468]
Coordinates
chr6:4520038-4520269:+
Coord C1 exon
chr6:4520038-4520082
Coord A exon
chr6:4520083-4520170
Coord C2 exon
chr6:4520171-4520269
Length
88 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
GACCTTTTTTCTTCCCACAGGGA
3' ss Score
12.13
Exon sequences
Seq C1 exon
GGCAACCCTGGAACAAATGGGCTCACTGGCGCCAAGGGTGCTACT
Seq A exon
GTAAGTACATCTGAGTAGCTGACTTGTGCTTAAAGAGGGAGGCCTCTACAGCCTGCTTTCTCCTGAGGGACCTTTTTTCTTCCCACAG
Seq C2 exon
GGACTCCCTGGTGTCGCTGGGGCTCCCGGTCTCCCTGGCCCCCGTGGTATTCCTGGCCCCGCTGGTGCTGCTGGTGCTACAGGTGCCAGAGGACTTGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029661:ENSMUST00000031668:18
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:
NO
A:
NA
C2:
PF0139113=Collagen=PU(20.2=60.6)
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:
GGCAACCCTGGAACAAATGGG
R:
ACAAGTCCTCTGGCACCTGTA
Band lengths:
143-231
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