MmuINT0039405 @ mm9
Intron Retention
Gene
ENSMUSG00000029661 | Col1a2
Description
collagen, type I, alpha 2 [Source:MGI Symbol;Acc:MGI:88468]
Coordinates
chr6:4470038-4470269:+
Coord C1 exon
chr6:4470038-4470082
Coord A exon
chr6:4470083-4470170
Coord C2 exon
chr6:4470171-4470269
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-Col1a2:NM_007743:18
Average complexity
IR-S
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(16.3=100),PF0139113=Collagen=FE(14.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(15.1=39.4),PF0139113=Collagen=FE(32.3=100)
Main Inclusion Isoform:
NA
Other Inclusion 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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: