MmuINT0040355 @ mm10
Intron Retention
Gene
ENSMUSG00000004098 | Col5a3
Description
collagen, type V, alpha 3 [Source:MGI Symbol;Acc:MGI:1858212]
Coordinates
chr9:20804870-20807754:-
Coord C1 exon
chr9:20807605-20807754
Coord A exon
chr9:20804984-20807604
Coord C2 exon
chr9:20804870-20804983
Length
2621 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TCCTTCCATGTCTGCTGCAGACC
3' ss Score
9.04
Exon sequences
Seq C1 exon
GCCCCCAAAGACGATGAACCAGAAACCCCTGCCCCTCGTCGTCGAAAGGGCAAAGGGAAGAAAAAAGGGCGGGGTCGAAAGGGCAAGGGAAGAAAGAAAAACAAGGAGACCTCAGAGCTGAGTCCGACCCCTGGTGCCCCTGAGAACCAG
Seq A exon
GTAAGAACCCGGAACCTTCTGCTTTGCTCTTCGCTGCCTGATGGCCACCCACCTCTAGCCCCTCATCTTTGTGTTGGTCCTCAGGGCCTGACTCCTGAGGTCTAATTCTCTCAGCGGAAGGGTATGGCAGGTCCTGTGTCAGGGGCTCTTTCATGTCTGTTCCACACTCTGTACTCGTGGGGAGCTAGAGGAGGAAGCACCTCTCAACACAAGAGGACCCCATGATTAGAAGGGTCATAGTGGAGTCCTAGTGGGGGATCATCAGCTCGGGTAACTGGTTTCAGGCGCATTGGTTATTGTGTCAGTATGTGGGGTTCACTGCTGGGGCCACCGGTGGGGATTTTTCCCTTGATGGCCCTGTTTGGAAACTCATCTGGAGGTTCTAGCAGGGGGCACAGACACTCCCAGCCCCCTGTCAGGGAAGGCTATCCTCTTTAAATTTGCACCTTTGGGAGCGACACATGGAGCAGCAAGGGAGGAAGGGGACAGCTGCCTATCGAGCTAGACTAGCAAAGTCAGTCCTGGAGACCAGTGTGATGACAGATGTCATATTCTGATCACCCTCACCTTTTTTTTTTCTTTTAAAAATGTTTTATTTAATTTTTTAAATTGGATATTTTCTTTATTTACATTTCAAATGTTTCCCCCTTTCCAGGTCTCCCCTCCCCACCCTTACTTCTTGAGGGTACTATTTAGGATTGCTGGTTGAGGAGGTTGCTCATTAAGGTGAATATGTAAGGAGTTCCTAGCTGGAGGTCTTCCCTTGGAGGCCTAGTTGGAGGCCTTTGGTAAAGGTCGTTGATAAAGGTCACTGTTGATATTTTGACTGGTCTTTGTTGTGTGTGAACTTTTCCCGGTAGACATGAGCAATAGATAGGGAAGTAATGGCCAACCAAGGTATGATTTCACTCAAATCTAGCTTGGGAAACCGTACTTACCGACAGCTAAAGTGAGGCGTTCCGTACTGGGGTGTGGTGACCCCTAAGCAGTCTCCCTAAGCATGGCTACCGAATTTCCCCTTAGCTGCACAGATGGAGGGCCCACAGTTAGCCTCCACACTCAGCACTCTCACCTTCCCAGAGACCAGGAGACCACGTGCATCCTGGGCAGATTACAGATAGCTGGGAGGGGCCCAGAAGAGAGTGGCTGGCATCTCAGATGAGGAGCCCATGCCTGCCTCCGACCTCTTTCCACAAGGGAATGGCACAGGCTGGGCCTTGAGGGTCTTTCATACCTACAGTTGCCTTTGATGGCAACACTGTCCCCTGACATGACTCATGACAGCCTGTAATTCCAATTAGAAGGAATCTGACGCCCTCCCTGCTCAGGGGACCTGCACTCACGTGTCGCATGTGTGAGTGTGTGCACGTGCACACATACATACACATTTTTAAAAAATCAAAAAGCGAAACAACAAAAACCCCTGTCCTGATCAAAAGCAACTTAGAGGAGAGAGGGGTTATTTCGGCTTACATTCCAGGTTACAGTCCCTTGTCTGGGGGAACTCAGGCAGCAACTTAAAGCATTGCATCCACAATTACAAGCAGAGAGAGGAAATCCATGAGTTCCCGCCTGCTTGCTCGATCTCAGCCAGCGCTGGCTGTTCTTAAGCTGTTCAGAACCTCCTGTAGGAGGGGCCAACTACAGTAGGCTGGATCTTCAGTTAACACTCAAGACAACCTTCCAGAGACAGCCCCCTGGCCCACCTCGTCTAAACACTCACAGACATCCTTCCCGGGTGACTCTAGGCTGTGTCAGGAGGCCATTTAGATAAGCCAATGCACTAGTTGAATGTTGAAGGTTAAGGGTTATTAATTAGGGAGATTGCTAGAAGACATAATGGGGTCATTGTTAGTGGAATGCTTAATTGAGGATCCCAGAGAGGGTTCATTATTTAGGGGGTCACTAAATAGTGATTTTTGTTGGAGGATTCTACTACTTGGGGTCATACTTGAGTCCCTGGATGAAAGGCTTTCTCTTCAGAGCCGTCGACGGGAATCATAAAGGCAGGCAGGGCTCACTCAGCTTGGAATAATTTGGGTTAATTGTGTAGGTTATTGACTGGTAAATTACTGGGCAGGGGTCCTAAGTCATCGGTTGGGTCATTGCTTGAAGTCCTTGGTTGGAGGGGTCACGGGTTGTAATTAGATATCAGTTCTGGATCTTTCTGTCCCACAGTATGACTACCAAGTTCTCTGCCTTGACCCAGTTCTTCTGCAGCTGTCCAGGTTGGATGAGTTGCAGCCTGGCTGGCTGATGGCTGAGTTGTCAGGGGAGAAGACATGTGGGGCTGGGCTTCCGGGAGTCTGGCCCCGAGTGCTGGCTTTTGACTTTAGCCACTGGGCCCTGGAGCCAATCTAGTTCTGCTCCCAGGCCTGGGAGATTTGGCCCTGCTTTGCTCCTCTTGTATCCAAGGAGGTTTCCCCTCTGGCCACCTTGGGCAGGTTGTACGGGGCACCTGTCTTTTCCCCCACCAGCCTCTAAATTTGCCGAGAAGCTACCTCTGTCTACTCACCCCTGAACTGGGGATTCCCCTAAGGGAGAGCCCTGGCTCCTCCTTTGTTTCCTTTGTCTTGATTGGCCTCACCCCAGATCTGACACTCCTTCCATGTCTGCTGCAG
Seq C2 exon
ACCTCCCTCCACATCCCTGAGACAGAGAAGACAGTTCCCCACCTGCCTCTGACTCCCACACCTCTGGCCATCACCACCACTGTCACGATTGGACAAAATGCCACAGTCTCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004098:ENSMUST00000004201:6
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:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
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