MmuINT0040499 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108855790-108856555:+
Coord C1 exon
chr9:108855790-108855877
Coord A exon
chr9:108855878-108856374
Coord C2 exon
chr9:108856375-108856555
Length
497 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
ATCTCTCCTCCCTGCTTCAGTGA
3' ss Score
8.27
Exon sequences
Seq C1 exon
ATGAGGCTGCGACTCCTGGTCGCTGCGCTCTGCGCTGCAGAGATCCTGATGGGAGCGCCGGAAGTGTGGGCCCAGCCCAGAGATAGAG
Seq A exon
GTGGGCATCTTTCGGGGCTCAGCACCCTGTCTGTCACCTATGCATCTACTCAAACTTTATCCCTGACACCTTTCCACCGATGAGTCCCCCAAACTCTTCGTGGATTCTTCCTAAACTCCCTGAATTCTACTCTGCATTCCCCAAATTGCCTCCTATCCCATATGGCACACAAATTCTAGCTCCCTGGATGCAGGCTGATCCTCTGTCCTCAGCCACCGGACAACAGTCCCTCCACGCTGATTTCAGCCCCGCAGCTACACCCCTGCTTGCAGGTTATCCTCCCCCAAGGTGCTCCTGCCCTCCCTGAGAAGCTCTGTTCAGAGTCCCACTGCGGTTTCCTCCAACACTGGCAGAAATACGCCTACCTGGGCTCCGTTTGCAGAGGAACATAAAGCCTATTGTCCTTCCAGTCCCCAAGTCCCAGGGGACCTCAGTGCCTAGAGGATGGTGGGTGGCTGTATTCCCTAAAAGGTCATGATCTCTCCTCCCTGCTTCAG
Seq C2 exon
TGACCTGCACACGCCTTTATGCTGCTGACATCGTGTTCTTACTCGATGGCTCGTCGTCCATTGGCCGCAGCAACTTTCGAGAAGTGCGAGGATTCCTGGAGGGGCTGGTGCTGCCTTTCTCAGGAGCAGCCAGTGCACAGGGCGTCCGGTTTGCCACAGTGCAGTACAGTGATGATCCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(29.3=83.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGAGGCTGCGACTCCTGG
R:
TGTGGATCATCACTGTACTGCAC
Band lengths:
269-766
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: