MmuINT0040209 @ mm10
Intron Retention
Gene
ENSMUSG00000026837 | Col5a1
Description
collagen, type V, alpha 1 [Source:MGI Symbol;Acc:MGI:88457]
Coordinates
chr2:27995861-27996913:+
Coord C1 exon
chr2:27995861-27995914
Coord A exon
chr2:27995915-27996868
Coord C2 exon
chr2:27996869-27996913
Length
954 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
CCTTTTCTCTCCCACCACAGGGC
3' ss Score
11.06
Exon sequences
Seq C1 exon
GGCCCGCGGGGTGAACGAGGCCCACGAGGCATCACGGGGAAGCCTGGCCCTAAG
Seq A exon
GTATGTTCCTGCTCCTTCGAGGCAGGAGAGGGAGGTCAGTGGCCTTTTCATGTAACAACAATAAAAAGAACAGTTTTCTTGAACATCAGTAAAGGGATTCTGCCTGCTAGCATCCTTCAACAAACTTCAGCAAACATGGCTGAGGGTAACCCCCAAAAGACCCAAGACAAACAGAGGAAGGACAGCCCCCCCCCCCCCCGTTTTTGTGTAGCTTCAGACCCAGGAAGCCACCAAGGTCTGGTGGGGAAGCCTCGTTGTTTTTTGTTTTTGTTTTTTTCTGGTAAAGATGGCTGGGGACTGTAGAGTTCTTTCTTAGAAGGTTCTTTCTGGTACAGGCAGAAACTCTGCCTACCCCTGCAAGGACCCCCCTCATGCCCAGGAATGAAGCAAGCTCCCCCTGCTGTAAATCTAGGGGAAAGCCAAGCATGGCACAGCTGTCCGGTTCTAACCAGTAAAAATCACGAATAGGGGGCTGAAGAGGCAGAAGACCAAGGTTTGGTTCCCAGCGCCCACATAGTGGCACAAAACCATCTGTCACTGTAGTTCTGGGAGATCTGATGCTGTCTACTGCAGCACCAGGCATGTGCTGGATGCACAGACAAAACAGCCATGCACATAAAAATTAAAAAAAAATAATTCCTCAGGGGGGGTGTGTGTGTTACTGAGAGGAGATTCCAGTTAGCTGACCCATCCCTAACAGAGAACCAGCTGGGTGCATGGAATGGTCCTGAAGCTGAGCCTTATGTTCTTCAAGTCATTTTTTATGTGTTCTTGGCTGAGCACAGCCTGTGTCCAGCTAGTCATGGGGACCTGTTCTGGAAATGTCCCGATCCTGCTCATGCAGGCTCCATAGTTGGCTGTGCATAGAGGCAGGCTAGCACTGCTGCCACACTGCACTGGGGTCAGGATGACCTTGGGAGAGCAATCATGGTGACCTTTTCTCTCCCACCACAG
Seq C2 exon
GGCAACTCCGGAGGTGATGGCCCAGCTGGCCCTCCTGGTGAACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026837:ENSMUST00000028280:34
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(21.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(14.1=73.3)
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