MmuINT0040249 @ mm10
Intron Retention
Gene
ENSMUSG00000026042 | Col5a2
Description
collagen, type V, alpha 2 [Source:MGI Symbol;Acc:MGI:88458]
Coordinates
chr1:45421221-45421997:-
Coord C1 exon
chr1:45421944-45421997
Coord A exon
chr1:45421275-45421943
Coord C2 exon
chr1:45421221-45421274
Length
669 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
ACCCCCTCTTTCACATTAAGGGT
3' ss Score
8.42
Exon sequences
Seq C1 exon
GGTCCAATTGGTTCTCGTGGACCAGAGGGCCCACCTGGGAAGCCCGGAGAAGAT
Seq A exon
GTAAGTTTCTATAGCACATTGCTTTGGAGTCTGAAAGAGGCTAACAGGGAGCTACAAGGGTCAGGAGAGTATTCTGTTCTGATTCCTATTTCATTTCCTCATTCCTCCAGCTCTTATTAAATCCACTTTAAAATGTAGAACACAGGTTAAGGTTTTCCAAAATTAGAAAGATCTCATTATTATGAGAGTGCTAAATTATTAAATACTATCTCTATGATGTCCTCCAAGATTTTTATTGATATTTATCTTTGAAAACAAACAAAAAAAACTACAACATTTTGTCTTTTAGAAGGCTGAAAAGATGACTTACTTTAAACATGGAACACATGCTTATTTTATTTTACTTTTTTACTGTGCTGGAATCAAACTTGGGGGATTTTTCATGATAGACAGGGTCTCTACCTTGAGCTGTGCCCCAGCCCTTTGCATGTAAATTCTGATGTTCTGAAAGTGTTAGATCAGAACAGGTTATTTTGCACCCATCTCTTATCATTGATAACTTAAAACACTAGGATTAAATGTTACCAGAGATAGAGCCCGGGTTTTGTCTTTACAGTTTGCAGCATAACACAAAAACTTGCTATAGATATATCATCTGTAATTTGTCATGTAATCTCAGAGAATAGTATTTAATCTCTCTATACCTCTCACCCCCTCTTTCACATTAAG
Seq C2 exon
GGTGAACCTGGAAGAAATGGGAATACAGGTGAAGTGGGATTCTCAGGATCACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026042:ENSMUST00000086430:11
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(25.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.6=38.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
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
- 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