MmuINT0040276 @ mm9
Intron Retention
Gene
ENSMUSG00000026042 | Col5a2
Description
collagen, type V, alpha 2 [Source:MGI Symbol;Acc:MGI:88458]
Coordinates
chr1:45449660-45449951:-
Coord C1 exon
chr1:45449898-45449951
Coord A exon
chr1:45449714-45449897
Coord C2 exon
chr1:45449660-45449713
Length
184 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
ATGTAAAATCTACTTTGTAGGGT
3' ss Score
5.57
Exon sequences
Seq C1 exon
GGTCTTCCAGGTCCCTTGGGACCTCCAGGTCCTGCAGGCCCTACTGGAGAAAAG
Seq A exon
GTAAGTTAGAAGGTATCAGTGTGCACACCAAAATAACAAGGCCTAAATTGTTGCTGTTTCTCAAGACTGTGGTTGAGGTAGACCATTTTAGAGCTTGCCTCACACTGTCTACCTTCAGATGTGCCTAGTAGTCTCCAATTGTATTTTGGATTAGGTACTTAGCTATGTAAAATCTACTTTGTAG
Seq C2 exon
GGTGAACCTGGTCCTAGAGGCTTAGTTGGCCCTCCTGGCTCCCGTGGCAATCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026042-Col5a2:NM_007737:36
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(20.0=100),PF0139113=Collagen=FE(20.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(3.5=16.7),PF0139113=Collagen=FE(20.2=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:
GGTCTTCCAGGTCCCTTGGG
R:
GATTGCCACGGGAGCCAG
Band lengths:
106-290
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: