MmuINT0040299 @ mm9
Intron Retention
Gene
ENSMUSG00000026042 | Col5a2
Description
collagen, type V, alpha 2 [Source:MGI Symbol;Acc:MGI:88458]
Coordinates
chr1:45479231-45480571:-
Coord C1 exon
chr1:45480527-45480571
Coord A exon
chr1:45479285-45480526
Coord C2 exon
chr1:45479231-45479284
Length
1242 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TCATTTGTTCTCAATTTTAGGGT
3' ss Score
12.73
Exon sequences
Seq C1 exon
GGTCCTGTTGGCCCAAGAGGACCTCAGGGTTTACAAGGACAGCAA
Seq A exon
GTAAGTGTTTTTATAATTAATTTATATGGTATAACATAAATAAAGGTCACAAATAAGCCTCATGTTTCATGACTACTTTAGACAGAACATTAAACTTTAGAATTCTCACCTGGAAAGGCATCTACCAATTAATCCTTACCGATAAAGAAGGACATGCAGCTTTCTTTTTTCATAGTTTATTTTTTAAAGTAATGTGTGTGTGTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTAGACCAGAGACTGAAGTCATGTATGTTATTTGTTTCTTGAGGCAGTCAGATGAGTGGTTTGCTCCAGAGGTGCCTTGTTCCCATTTCTGTTTACCAAGCACTGGGATTACAGAATGGCCACTATATCTGCTCAGATTTTACATGGGTGGTAGAGGCCCACAGTCTAATCCTGCCCATGCCTGCAGAGAAAATGCTTAATCCACTGAGATGTCCTCTAGCTCTCACAGTTTCTTACTTGTCCTGCATATTCATCATCTAATTTCTTTATATGACTCACCTCTAACACTAGGAGTTATGTTATGTGTCTTTGGTTCTAAAATAACAGAGCATTATTTCATGTCCTATAAAGTTCCCATAATTGATTTTTTTTCTAAGCCTCTGGCTTTACAATAAGATAATAAAAGTTCACTTGAAATTAGTATTCTTGTAAATTAAAATCAAGGTGGTTATTCTGTGGAATCTTGCTTGAAGAATATTCTAATACTATGTAGTTCCTTTCCACACCTACCAAATGTCAGTAAAACTATGATGTAGAACTATTTTACTTTGTGTAATGATTTAATGGGTATTAGCTAATAATATTTCAAAAGAAAAAAATCTTTACCTCAATCAAGGTAATCACATTGTCATGATCATCTGTATGGACTTTTCTGATGGTAAGTACTGTTGTCTGAGCACCCATTCTGTGGTAGCACTAGTCTATTTTAACACAAATTTATCTAAACAGACCAATGAACTAAGTCTTAATCTTAGTCTAATTTTTCATAATGAAATTACATTATATTCAGTGTCAATAATTTATTAAAATTATGTATCTGGGAAGTGTCAGAGACAAATATCAATATTGTACCTTGTCAAAAGTACAGAAATTGGTATGTTGCTTTCCTTTGCTTCATTTATCATTTGTTCTCAATTTTAG
Seq C2 exon
GGTGGTGTGGGACCCGCAGGACCTCCTGGTGAGCCTGGCGAGCCTGGACCAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026042-Col5a2:NM_007737:9
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(18.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(22.7=100)
Main Inclusion Isoform:
NA
Other Inclusion 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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: