MmuINT0040446 @ mm9
Intron Retention
Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:105922933-105923132:-
Coord C1 exon
chr9:105923097-105923132
Coord A exon
chr9:105922996-105923096
Coord C2 exon
chr9:105922933-105922995
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-Col6a4:NM_026763:27
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=PU(12.9=66.7)
A:
NA
C2:
PF0139113=Collagen=FE(32.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: