MmuINT0040524 @ mm9
Intron Retention
Gene
ENSMUSG00000025650 | Col7a1
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108861282-108861679:+
Coord C1 exon
chr9:108861282-108861401
Coord A exon
chr9:108861402-108861535
Coord C2 exon
chr9:108861536-108861679
Length
134 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGA
5' ss Score
6.66
3' ss Seq
ATCTCCGTCCTTGATCCCAGGTC
3' ss Score
8.6
Exon sequences
Seq C1 exon
ATCCACTGGGCCCAGTGAGGAGAGTCCACTTGACTCAGGCTGGCAGCTCATCTGTCAGCATCACCTGGACTGGGGTTCCCGGTGCCACAGGATACAGGGTTTCCTGGCACTCAGGCCATG
Seq A exon
GTAGGAGGCAGGGGTTTAAGGAGGGCTCTGGGAGGAGGTTCTGAATACAGTGGAGGCTAAAGATTCTTTTGGGATCCAAGTGGAGCATTGGGCAGTCGGACAAGTCCTGGGGTTATCTCCGTCCTTGATCCCAG
Seq C2 exon
GTCCAGAGAAATCTCTGTTGGTTTCTGGAGATGCCACGGTGGCTGAAATAGATGGGCTGGAGCCGGACACAGAGTATATAGTGCGTGTGAGAACCCACGTAGCTGGTGTGGATGGAGCCCCCGCCTCTGTGGTTGTGAGGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650-Col7a1:NM_007738:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.195 A=NA C2=0.184
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(46.8=90.2)
A:
NA
C2:
PF0004116=fn3=PD(51.9=83.7)
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:
CCCAGTGAGGAGAGTCCACTT
R:
AGTCCTCACAACCACAGAGGC
Band lengths:
253-387
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: