MmuINT0040234 @ mm9
Intron Retention
Gene
ENSMUSG00000026837 | Col5a1
Description
collagen, type V, alpha 1 [Source:MGI Symbol;Acc:MGI:88457]
Coordinates
chr2:27872946-27874068:+
Coord C1 exon
chr2:27872946-27872999
Coord A exon
chr2:27873000-27873960
Coord C2 exon
chr2:27873961-27874068
Length
961 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
ATGGCTCTATTTCCTCACAGGGC
3' ss Score
9.06
Exon sequences
Seq C1 exon
GGTCCTCCAGGACTCCCTGGCCTCAAAGGAGACTCCGGTCCCAAAGGTGAAAAG
Seq A exon
GTGAGCTGAGACTTAGGGGACCCTAGCATTGCAAGAACAGCACCCTGACTCAGACTTAGGGGACCCAAGCATTGCAGTAACAGCACCCATGACTCCATCCCAGGAGTTACTGACCCACTGCCAAGTACCTGCTGTGGCTCTCATGGGATGCTAATGTAGAGCAACGGAAGAGAAATACTCACAGGACTCTGAGACTCATGTCTGTATGCCAGCATTGACAAGAACCTGCTAGAGCCCTGGTGGCTTCATTAACAGATGGTGACTTTTCTCCTTCCATCGATTTATTTGTAAATAAACGAGCTCACAAGACAAACAGCTGCTCACAGAGAAGGCAACAAGAACGTCCTTTCGACTCGGAAGTCCTCCCAGAACACTGTAGATGCTCACACAAAACCAAAAGACGTATGAGGCAGATGTGGGGGCTTTTTCTCCTGAAAGGTGTTCAGATGAGTCTATTATCCTCAGTTCTCAGCAGTTTCCATCCCGTGTCAGCCTTGGGCCTTGCAGGAAAAAGGTGGCATGCTTACCGAAAGTCAGAATGTTTCCTAAGTAAAAACATAGACAGAAACTATCAGGAGAATCCCATGGTCTCTGGATCTGGGTGCCCGTCGGCTTCTTTTTGGTTGTTATTGGGGCCCAGTGCCAGGGATGGTGGTGGCTCACTGCCAGGGATGGTGGCAGTACTGTAAACTGAACCCAGAGCCCCATACATGCTGGTCAAATGCTTCACTGCTCAGCCATACCCTGTCTCTCCCTGAGTGTTTTTGCAAATACATTCCTTACTAGCAAGGGGCCAGGAGACTCGTCACCTGTCCTGTCTCTGCTTACTTTCACTCCCCAACATGTTGACTGTGATATGTTTCCCTGAGCTGTGGCTATGAGCCCTGTCACCCCACCCACTGTGCAGTGGACTCAGGGTACTGGTAGCATAGATACCTATCATGGCTCTATTTCCTCACAG
Seq C2 exon
GGCCATCCAGGCCTGATTGGACTCATCGGCCCTCCGGGAGAGCAAGGTGAAAAGGGTGACCGTGGACTCCCAGGCCCCCAGGGTTCATCTGGTCCTAAAGGAGATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026837-Col5a1:NM_015734:57
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=0.901
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(20.7=100),PF0139113=Collagen=FE(24.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(3.7=8.3),PF0139113=Collagen=FE(50.0=100),PF0139113=Collagen=PU(7.9=13.9)
Main Inclusion Isoform:
NA
Other Inclusion 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: