MmuINT0040607 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108878216-108879160:+
Coord C1 exon
chr9:108878216-108878260
Coord A exon
chr9:108878261-108879124
Coord C2 exon
chr9:108879125-108879160
Length
864 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
ACGTATTTCTTATTTTTTAGGGT
3' ss Score
11.31
Exon sequences
Seq C1 exon
GGTGAAGCTGGCCGTGCAGGAGGACCTGGGGACCCTGGGGAAGAT
Seq A exon
GTAAGTCTGGGCTCTGGGCAGGACCAAGCCTGGCTTGACCATGAAAACAAAGACCATGCTTGGGGTTGTTCATAGCGCTGAACCCTTACTGCCTATGTTCTTGGGAAGTTTCTGCTTGGAACACATAGCACACAGCTGCACGCTTTTTGGTTTCCTTATTTGTGGACTTCCATACTTGTGAACGCCAGCTTGGCTTCTGTGCACCCATCCTTCATCATGGTTCCTTACCATGACTGAACCCATGCAGGTCTGATACTGCCTCATCTCCCAGGTCTCAGGATGCAGCAGTATCTCTGTAGGCCTCTCCTTGGCCACGTGTTTCTAATCTTGTGTTCCACCCCCATCTGTCTGAGTATTAATCTGTGCTCACGTCTAAGTTTCCTGATGGAGTTTCCATTGAGCGCCACATCTGTGGCCCTTCCTATTCGCCTGCTCACGTGTGAGCTCTGTGTGCCTGTGGTCACGGCTGAACTCCCACGTGTCTGTGGTCACATCTGGGCTTCCCTTGGCCTGTGTTCTCACAAGCCTATGGTCCAGTCTGTGTTTCCAGAGGCCCGTAATTATCTGAGTTCTCTTGTGAATATTTTTGGTCCATAGAGAAGCTTGGTATTAACATTCTTATACTATTAAAAAATGTGTATGAGTGTTTTGCCTGCTCGTTTGTGCACTACCTGCTTGTCTGTTGCCTTTGGAGGCCAGAGAGGACATTGGATATCTTACTGAAGTTGTAGATAGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACCCAGGACCTCTGGAAGAACAGCCAGTGCTCTTAACCTCTGAGTTATCTCTCTAGCCTGAATTACTTTATATAGACACGTATTTCTTATTTTTTAG
Seq C2 exon
GGTCAAAAAGGGGCTCCAGGACTCAAAGGTCTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:91
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=FE(26.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.8=100)
Main Inclusion Isoform:
NA
Other Inclusion 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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: