MmuINT0039410 @ mm9
Intron Retention
Gene
ENSMUSG00000029661 | Col1a2
Description
collagen, type I, alpha 2 [Source:MGI Symbol;Acc:MGI:88468]
Coordinates
chr6:4471231-4471494:+
Coord C1 exon
chr6:4471231-4471284
Coord A exon
chr6:4471285-4471395
Coord C2 exon
chr6:4471396-4471494
Length
111 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
GATGCCTATCCTTCTAACAGGGT
3' ss Score
9.05
Exon sequences
Seq C1 exon
GGCAGCCCTGGTTCTCGAGGTCTTCCTGGAGCTGATGGCAGAGCTGGTGTAATG
Seq A exon
GTGAGTCACTCATCACTTACTTTCCAGGAAGGACCTTGATAATGCTGGTGCCAGATGTGTCCTCAGCATTACATGAACAGCCTCCTTATTTGATGCCTATCCTTCTAACAG
Seq C2 exon
GGTCCTCCTGGCAATCGTGGTTCAACCGGCCCTGCTGGAATCCGAGGTCCTAATGGAGATGCCGGTCGACCTGGGGAACCTGGTCTCATGGGACCCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029661-Col1a2:NM_007743:22
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(23.6=100),PF0139113=Collagen=FE(20.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(6.9=15.2),PF0139113=Collagen=FE(38.1=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:
CCCTGGTTCTCGAGGTCTTCC
R:
TCTGGGTCCCATGAGACCAG
Band lengths:
148-259
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: