MmuINT0040228 @ mm9
Intron Retention
Gene
ENSMUSG00000026837 | Col5a1
Description
collagen, type V, alpha 1 [Source:MGI Symbol;Acc:MGI:88457]
Coordinates
chr2:27869627-27869943:+
Coord C1 exon
chr2:27869627-27869680
Coord A exon
chr2:27869681-27869889
Coord C2 exon
chr2:27869890-27869943
Length
209 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
CAATTTTCTTGTTCCCACAGGGT
3' ss Score
10.79
Exon sequences
Seq C1 exon
GGCCCTGTGGGCTTTCCTGGAGATCCTGGTCCCCCTGGAGAGCCAGGCCCCGCA
Seq A exon
GTAAGTGTCCATCTTGTCTCTACTGCCTCTTGTCACCCCCAGTTTTCCTGCTCTCTGTTTCCTCTCCTCTCCTGGGTTCTCCGGGGCGCAGCACCTCTCCAGGCTGTCCCTGTTCCAATGCCCAGCCCGTGGGAGAGGACCTGAGGACACACTTGGACTGGAGGATGAACTTCATCTGTGCAGTGGAAACAATTTTCTTGTTCCCACAG
Seq C2 exon
GGTCAAGACGGCCCACCTGGTGACAAAGGGGACGATGGTGAACCTGGGCAGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026837-Col5a1:NM_015734:51
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:
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: