MmuINT0040304 @ mm9
Intron Retention
Gene
ENSMUSG00000004098 | Col5a3
Description
collagen, type V, alpha 3 [Source:MGI Symbol;Acc:MGI:1858212]
Coordinates
chr9:20605660-20606294:-
Coord C1 exon
chr9:20606211-20606294
Coord A exon
chr9:20605717-20606210
Coord C2 exon
chr9:20605660-20605716
Length
494 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGCTCTGTCTGTCTTTCCAGCTG
3' ss Score
11.61
Exon sequences
Seq C1 exon
TTCCATTTTGCAAGCAGCTCGATGAAGGGACCCCCAGTGTCCTTCCAGCAGGCCCAGGCCCAGGCAGTATTGCAACAGGCTCAG
Seq A exon
GTGAGTGGGGTAAGGGCCATGTGTTAAGTGAGGGACAGCATAAATAAAGGCTCGTGCAGGACTGGTTGGAGACCGAGGATATCTCTCTCCTGAAGATGCTTGCTGTGAGTTTCTGTTGTTATTGTAAAGTCCTGAGCCTGGGTGGTTAATGGAGAACAGAGGATCCAGGCTAATGATTCTGGAGGCTGGGAAGTCCCAGAGCACCATGCTGCCGCCTAGCTGGGTGCATTGTAACTGGTGGGGGGCAGTGCAAGGCAAGATGGTGCATACATGAGGATAAGCCTTACTCTCCTAAAGGTACTGATTGTCAGGATGGGGTACCCCACCCTTCTGATTTCACCTAATCCCAATCATCTTCCAAAAGGCTCCCCTCAAAGTGTTATCAACACATGAATCGGGGAAGAGATTTACAACCTGTGGAGGAGGCACACTCCTACCTCTAGTAGTGATTCTGTGGTCTTATGGGGGAACTCTTGCTCTGTCTGTCTTTCCAG
Seq C2 exon
CTGTCCATGAAAGGGCCCCCTGGTCCAGTAGGGCTCACTGGGCGCCCAGGCCCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004098-Col5a3:NM_016919:13
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:
PF0139113=Collagen=PU(26.6=89.5)
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: