MmuINT0040216 @ mm9
Intron Retention
Gene
ENSMUSG00000026837 | Col5a1
Description
collagen, type V, alpha 1 [Source:MGI Symbol;Acc:MGI:88457]
Coordinates
chr2:27859381-27859615:+
Coord C1 exon
chr2:27859381-27859470
Coord A exon
chr2:27859471-27859561
Coord C2 exon
chr2:27859562-27859615
Length
91 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
AAATTCTTACTGCTTCTCAGGGA
3' ss Score
5.88
Exon sequences
Seq C1 exon
GGTGACCCAGGTCCTGCTGGCCTCCCTGGGAAGGATGGCCCTCCAGGATTGCGTGGATTCCCTGGGGACCGAGGGCTACCTGGCCCCGTG
Seq A exon
GTGAGTGAGGGGCCAGGTGGGTGTAGTGGTATGGCACACAGCCCTAGGGCTCTGTCTGAGGCCCTCAACCTAAATTCTTACTGCTTCTCAG
Seq C2 exon
GGAGCCCTTGGACTCAAAGGCAGTGAAGGCCCCCCTGGCCCACCAGGTCCTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026837-Col5a1:NM_015734:40
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(38.7=100),PF0139113=Collagen=PU(2.1=6.7)
A:
NA
C2:
PF0139113=Collagen=FE(22.7=100),PF0139113=Collagen=FE(17.7=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:
GGTGACCCAGGTCCTGCT
R:
GCCTTCACTGCCTTTGAGTCC
Band lengths:
120-211
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: