MmuINT0040345 @ mm10
Intron Retention
Gene
ENSMUSG00000004098 | Col5a3
Description
collagen, type V, alpha 3 [Source:MGI Symbol;Acc:MGI:1858212]
Coordinates
chr9:20776992-20778530:-
Coord C1 exon
chr9:20778477-20778530
Coord A exon
chr9:20777100-20778476
Coord C2 exon
chr9:20776992-20777099
Length
1377 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
TGATCTCTGTTTCTGCAAAGGGG
3' ss Score
5.68
Exon sequences
Seq C1 exon
GGTGAGCCAGGGGATGCTGGAGACGCCGGACCCCCAGGAATTCCCGGCATCCCT
Seq A exon
GTGAGTCTGTAGAGCATTGCCCTTGTACTTGCCATAGGGAACTGCTGACCTAGAGCGTGTCATGCTCTCATGACCTCCAGGCAGTCCTTAGAGCATTGCTGAATCCAGACCAACAGATATCCCTGTCTGTTGTGAAAGATATGAAAGATGCTCCACCTGAGAAGATCTCAGGGGTGCTTTGTAGAGTCCCAAAAGTTGCCCACAAGCACACAGGGCTGAGGAGACAGCTAGGGGTTTAAATCAAAGCAACAAACATGGAATTGGGGGTAAAGCTGCCCAAAGGGGGACCATTTTCTTATGTACCCAAAGGCAGGACATAGGCCAGGACAGACTAATCATGGGTGACAGATCCATTATCCCTAACTCAGCTAGTTCTAGTTCTCTGTGACCTCTAACACTTGCATTACCTAGGCTACCTGACTCTGTGTGCATGTGTGTGTGTGTGTAAATGCACTGCCCAAAGACTAGAAGATGACATCGGATTCCCGTGGAGCTGGAATTGCAGGTGGTTGTGAGATACCTGATGCGAGTGCTTGGAGCTCCGTTTTTGGTCTCTGCATGAGTAGTATGTGGTCTGTCTTAGTTAGGGTTTCCATTGCTGTGAAGAAACCCCATGACCAAGGCAGCTCTTATAAAGGACAACATTTAATTGGGGCTGGCTTACAGGTTCTGAGGTTCAGTCCATTATCATCACAGCAGAAAGCACGGCAGTGTCCATGCAGGGATGGCTCTGGAGGATCTGAGAATTCTACATCTTCACCCAAAGGAAGCCAGGAACAGACTAACTCTTCTGTACTGGGTGGAGCTTCAAAGCCCACCCCCACAGCGACACACTTCCTCCAACCAGGCCACACCTCCTAACAGTAATAGTCCCTATGGGCCAAGCATATTCAAACCACCACATGCTCTTAACCACTGAGGCACTTTCTAGCCCTGATACATATACATATACATATACATATACATATACATATACATATACATATACATATACATATACATATACATATACATATACACATACACATACACATACACATACACATACACATACACATACACATACACATACACATACACATACACATACACATACACATACACATACACATACACATACACATATACATATACACACACATACACACACACACACACACACACACACACACACACACATATATATATATATTCATTATTGTGTGTGTGAGAGTGTGGCACATGTGTGGAGGTCAGAGGACAGCTTTTGGAGGTCAGTTCTCTTCTACCATGGGGTCTGGGGATGGAACCCAGATTGTCAGACTTCCCAGGCAAGGTGTGTTCATCTTTGGTCCATGACACTCTGACCTTTGACTCCTGATCTCTGTTTCTGCAAAG
Seq C2 exon
GGGCCCAAAGGTGAAATTGGTGAAAAGGGGGATTCGGGTCCATCAGGGGCTGCTGGTCCCCCAGGCAAGAAAGGACCCCCAGGAGAGGACGGCTCTAAGGGGAACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004098:ENSMUST00000004201:50
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(18.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(38.5=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:
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