MmuINT0040536 @ mm10
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108962600-108962900:+
Coord C1 exon
chr9:108962600-108962772
Coord A exon
chr9:108962773-108962864
Coord C2 exon
chr9:108962865-108962900
Length
92 bp
Sequences
Splice sites
5' ss Seq
GAGGTTTGG
5' ss Score
3.53
3' ss Seq
AGGAGCGTCTTTGTCCACAGCCG
3' ss Score
6.63
Exon sequences
Seq C1 exon
GGCTTAAGGTGATGGCACTGAGTTTGGTGGGAGCTGACCCAGAGCAGCTGCGTCGCTTGGCACCAGGCACGGACCCCATCCAGAACTTCTTTGCTGTGGATAATGGCCCAGGCTTGGACAGAGCAGTCAGTGATCTGGCTGTAGCCCTGTGTCAGGCAGCTGTGACCATAGAG
Seq A exon
GTTTGGAGAAGGCCTCTGGGGACTGGTAGTACAGAGGGGACCTTGGGGTTCTTTTAGAACTTCCTGGTCTCAAGGAGCGTCTTTGTCCACAG
Seq C2 exon
CCGCAAACAGGGCCTTGTGCTGTGCACTGTCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.379 A=NA C2=0.833
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(25.6=77.6)
A:
NA
C2:
PF0139113=Collagen=PU(14.7=83.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGAGTTTGGTGGGAGCTGAC
R:
ACAGCACAAGGCCCTGTTTG
Band lengths:
179-271
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