Special

MmuINT0040592 @ mm10

Intron Retention

Gene
Description
collagen, type VII, alpha 1 [Source:MGI Symbol;Acc:MGI:88462]
Coordinates
chr9:108973813-108974109:+
Coord C1 exon
chr9:108973813-108973875
Coord A exon
chr9:108973876-108974064
Coord C2 exon
chr9:108974065-108974109
Length
189 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
TTAGACCAATTCTTTTACAGGGT
3' ss Score
7.11
Exon sequences
Seq C1 exon
GGTGTACCAGGCATCAAAGGCGATGTGGGAGAGCCTGGAAAGAGGGGTCATGATGGCAACCCA
Seq A exon
GTGAGTTCTTGCCCCATAAGTCACATGTGTGTGAGACCATGGCTCTTACATGTGTTGTCATATATGCAGGGCTGGAATCAGCACTGCTTAGGAGATAAGTTCTATCCTTGGCCATCGGGGGCAGGGTGGGCATGAAGAAGAGGGGGTTGGGTGTCAGGACAAGGTGCTTTTAGACCAATTCTTTTACAG
Seq C2 exon
GGTCTCCCGGGAGAGCGTGGTGTGGCTGGGCCTGAAGGGAAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025650:ENSMUST00000112070:79
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=1.000 A=NA C2=0.911
Domain overlap (PFAM):

C1:
PF0139113=Collagen=FE(28.6=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.0=100),PF0139113=Collagen=PU(17.5=73.3)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
LOW PSI
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGTACCAGGCATCAAAGGC
R:
GGCTTCCCTTCAGGCCCAG
Band lengths:
107-296
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Pre-implantation embryo development
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types