MmuINT0040525 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108861536-108862106:+
Coord C1 exon
chr9:108861536-108861679
Coord A exon
chr9:108861680-108861980
Coord C2 exon
chr9:108861981-108862106
Length
301 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TACCTTGCCTTTGTCCCTAGCTC
3' ss Score
9.12
Exon sequences
Seq C1 exon
GTCCAGAGAAATCTCTGTTGGTTTCTGGAGATGCCACGGTGGCTGAAATAGATGGGCTGGAGCCGGACACAGAGTATATAGTGCGTGTGAGAACCCACGTAGCTGGTGTGGATGGAGCCCCCGCCTCTGTGGTTGTGAGGACTG
Seq A exon
GTGAGTAGATCCCAGCCAGCTATTCCTTGGCTGACCCAGCCTGCTATGTCTTTCTGACTGCTGCCCCTGCTCAGTGCCCTGTCTATCCTGAACCTCCCAGGGTTACTGAGCGTCCATTCATGTTTGTGACCTTGGCCGTGCTACACTCCCCCCGAAACACTAACCTCCTCCCCTCAAAGTTCCCTCCACTGACCTGGCCACACTAACCTTGCCCAGCCTTCATTACCTATGCCTGCCTTGCTACTCTTGTTTCTGCTAGACCCCCAGTGGCCCCTCACTTTTACCTTGCCTTTGTCCCTAG
Seq C2 exon
CTCCTGAGCCTGTGGGCAGTGTGTCGAAACTGCAAATCCTTAATGCTTCCAGTGATGTTCTACGGGTCACTTGGGTAGGAGTCCCTGGGGCCACATCCTATAAACTGGCGTGGGGACGTAGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.184 A=NA C2=0.023
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(51.9=83.7)
A:
NA
C2:
PF0004116=fn3=PU(46.8=86.0)
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:
AGAAATCTCTGTTGGTTTCTGGAGA
R:
CGTCCCCACGCCAGTTTATAG
Band lengths:
256-557
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: