MmuINT0040238 @ mm10
Intron Retention
Gene
ENSMUSG00000026837 | Col5a1
Description
collagen, type V, alpha 1 [Source:MGI Symbol;Acc:MGI:88457]
Coordinates
chr2:28020768-28022334:+
Coord C1 exon
chr2:28020768-28020803
Coord A exon
chr2:28020804-28022280
Coord C2 exon
chr2:28022281-28022334
Length
1477 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
CTTTCTTGTTTTCCCTCCAGGGT
3' ss Score
12.28
Exon sequences
Seq C1 exon
GGCCCTCCAGGTCCCAAAGGTGCTAAGGGCTCTTCG
Seq A exon
GTAAGTGACTCTGACTTGTCTGGGCCCACCTGAGACTGCCTTGTAGGTGGGAGAGGAGTCTCCTAGGGCTGGACCCCCAACCCAGACCCCCCCACCCCAGACCCCCACCCCTACTCATAGCTGTACTCTCCCCACACCTTCTCTTTTCTTCTTCATTACACTGTATGTTGCTGGCATTTCTTGTTGTCTTTAGGTTTTCAGTTTTGTTTTTTTGTTTGTTTATTTGGTTGGTTGGTTGGTTGGTTGGTTAGTTTTTTTGTTTTCAAATAACCAATTGCTCTGCTCCTGGCTGTTTTTAAAGTATTATTTTAATCGTAGCTGTTCATGAGGTAAGGTGGGAGAAAATCAAGTGAGACTAGCTAGCTCTGACAGATCCTGCAGCCTCTTGACACTTTGGGCTAACATGGAATAATCACGTGTATTATGGGCCTTGGTGTGGCTTTTTTACTATGCTGGGGCCATTGGCGGTTCCATGGCTTTACTGATGGAGCCATCCAGCCTCTCTAGATATTCATGAAACCTAGCAGGCTAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGTCCCACTGTGCTACAGAATACACGGTTTTACTCCTGTGTAGCCATGTTTGGTACCCAGCACGTCTTCATCCATCCTCCCAGTGTTCCAGAGCCCTGCCCCTCCCCCAGCCTCTGAAACCACTGTCCTACCCTACCTCCTGCTTTCCATGAACTGTTAATGCTCCAAATTATCATACACTGTATTTCTGTTAATGTTCACTTCTGAGCGCCCCTCGTCTGTCTGTCCCCCTCCTCGTCCCTGCCCTGCAAACCCCCCCATTGCCCATGCAAAGACAAGATGGCCTCCTTTATGACTGAGCAACACTCCTTGTGTGTGTATAAGATACATTCCGTATTTACTCCCTGGATGGACGTCTAGGCTGACTCCACATCTCAGCTATTGTGGTCAGTGCAGTAGCCACATGGGTGTGTGAGCACCACTCAGACACGCTCAGACACACTCAGACACACTCAGACACACTCAGAGGTGGAGCAGCAAGCTCGAGTAGCATGTCTGTCTTTGGTTTCCAGCATGGCGGAGCCATTCTGCATTCGTACCAGCAGTGCCCCATCCTCTCCAGCACTTTTTGTCTTTCTGATAGCGGAGTTGCTGACTGTGTGGAAATGAAGGCCCACTGAGGGTTGGGCTTACATTTCCCTGATGGCCCACACAGCTGCCTTGCTTCCATAAGCCTGTTTGTTGGCATTTTTGTTTCCTTTGACCTCCGTCTCCTGTCTTTATAAATGAGCCTAGCCCATCTCAGGCCAAGGTGGCTGGGCCTGGCCTCAGGAGCAGAGAACCCTGCCTGCCTTGTCCCTTTGTCCCGGCCTTCTTGGAGCTAATAGGTCATTCAGAACACAGGAGGCCCCATGACCAAGTGCTGCTTTCTTGTTTTCCCTCCAG
Seq C2 exon
GGTCCCACCGGCCCGAAGGGTGAGGCAGGCCACCCAGGACTCCCCGGCCCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026837:ENSMUST00000028280:60
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(17.5=100)
A:
NA
C2:
PF0139113=Collagen=FE(27.0=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