MmuINT0040558 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108869039-108869270:+
Coord C1 exon
chr9:108869039-108869071
Coord A exon
chr9:108869072-108869216
Coord C2 exon
chr9:108869217-108869270
Length
145 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
ATAGCCTTTGTCACCTTTAGGGA
3' ss Score
8.59
Exon sequences
Seq C1 exon
GGTCCTGGTGGTGCTGGAGCCAAAGGAGAAAAG
Seq A exon
GTATGTCCGGAGGCTGTTAAAGGGGAGGTCAAGGTCACAGGGTCTATCTTGGGTCCGACCTAGAGATCACAGGCTTTGCCTGATGGCTGGGTTGTGGGAGTGCCTGGAGCCTGGTTCTAGTATTGATAGCCTTTGTCACCTTTAG
Seq C2 exon
GGAGAGGCTGGGCTCCCTGGGCCCAGAGGAGCTTCTGGAAGCAAAGGAGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:47
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(6.6=36.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTGGTGCTGGAGCCAAAG
R:
CTGCTCTCCTTTGCTTCCAGA
Band lengths:
82-227
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: