MmuINT0040276 @ mm10
Intron Retention
Gene
ENSMUSG00000026042 | Col5a2
Description
collagen, type V, alpha 2 [Source:MGI Symbol;Acc:MGI:88458]
Coordinates
chr1:45392815-45393106:-
Coord C1 exon
chr1:45393053-45393106
Coord A exon
chr1:45392869-45393052
Coord C2 exon
chr1:45392815-45392868
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:ENSMUST00000086430:36
Average complexity
IR
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(25.0=100),PF0139113=Collagen=PU(3.3=11.1)
A:
NA
C2:
PF0139113=Collagen=PD(5.9=22.2),PF0139113=Collagen=FE(28.3=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
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types