MmuINT0040446 @ mm10
Intron Retention
Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:106020602-106020801:-
Coord C1 exon
chr9:106020766-106020801
Coord A exon
chr9:106020665-106020765
Coord C2 exon
chr9:106020602-106020664
Length
101 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
CCTGCTTTTGCCTTGTTAAGGGA
3' ss Score
7.62
Exon sequences
Seq C1 exon
GGTGAACCTGGGTTCCCTGGCTATCCTGGTGTGCAA
Seq A exon
GTAAGAAGAGATCTCTGTGGGCCTGGCAACTGGTAGGCACTGTGTGTCACATGTGTGCAAATCTTTCTTCACGTTCATAACCCTGCTTTTGCCTTGTTAAG
Seq C2 exon
GGAGAAGATGGTAACCCAGGCCGTGGAGGAGAGAAGGGGGCCAAGGGAATCCGAGGGAAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032572:ENSMUST00000121963:27
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(12.0=75.0),PF0139113=Collagen=FE(16.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.5=52.4),PF0139113=Collagen=FE(30.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
AACCTGGGTTCCCTGGCTATC
R:
CCTCTTCCCTCGGATTCCCTT
Band lengths:
95-196
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