MmuINT0039404 @ mm10
Intron Retention
Gene
ENSMUSG00000029661 | Col1a2
Description
collagen, type I, alpha 2 [Source:MGI Symbol;Acc:MGI:88468]
Coordinates
chr6:4519830-4520082:+
Coord C1 exon
chr6:4519830-4519928
Coord A exon
chr6:4519929-4520037
Coord C2 exon
chr6:4520038-4520082
Length
109 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
CCTTCTCCTTTCTCTCACAGGGC
3' ss Score
12.77
Exon sequences
Seq C1 exon
GGTGAACTTGGGCCCGTTGGTAACCCTGGCCCTGCTGGTCCTGCTGGTCCCCGTGGTGAAGTGGGTCTTCCAGGTCTTTCTGGCCCTGTTGGACCTCCT
Seq A exon
GTAAGTAGTCGTTGACATAAGACAGTTGATGAGAAAGACTGAAGATAGGGTCATAGAATGTAAGAAATATTCTCGTTCAATGAGTTTTTCCTTCTCCTTTCTCTCACAG
Seq C2 exon
GGCAACCCTGGAACAAATGGGCTCACTGGCGCCAAGGGTGCTACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029661:ENSMUST00000031668:17
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:
NO
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:
GAACTTGGGCCCGTTGGTAAC
R:
TAGCACCCTTGGCGCCAG
Band lengths:
139-248
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