MmuINT0040170 @ mm9
Intron Retention
Gene
ENSMUSG00000031273 | Col4a6
Description
collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695]
Coordinates
chrX:137609162-137609572:-
Coord C1 exon
chrX:137609411-137609572
Coord A exon
chrX:137609261-137609410
Coord C2 exon
chrX:137609162-137609260
Length
150 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
TTTCCTTTGGCCCTTACCAGGCA
3' ss Score
8.31
Exon sequences
Seq C1 exon
GCCGCCCAGGCCCTCCAGGTCCTCCAGGTCCCCCTGGGCCATCCTCAGATCAAGGCGATCCTGGAGACTCTGGCTTCCCTGGGATTCCAGGCCTTCAAGGGTTCAAGGGAAACCAAGGACTTCCAGGTTTCTCTGGCCTCTCTGGAGAGCTAGGGCTAAAGG
Seq A exon
GTAAGTCTGTTCCACCAGCTTCAAGACCCATCAGTCACCACTGCACAGTCCAGTCGCCCTGAAGAGGCTCTCGATGGTGCTTTTTCTGACTGGTCCCCCTCTGTCACCATCATGCCAACACCTCACATGTTTTCCTTTGGCCCTTACCAG
Seq C2 exon
GCATGAGAGGGGAACCTGGCCTCATGGGGACTCCTGGCAAGATCGGGCAACCAGGAGACCCAGGATTTCCTGGGATGAAGGGGAAGGCGGGGCCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031273-Col4a6:NM_053185:39
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=PD(72.6=81.8),PF0139113=Collagen=PU(24.6=27.3)
A:
NA
C2:
PF0139113=Collagen=FE(54.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGCCCTCCAGGTCCTC
R:
CCTTCCCCTTCATCCCAGGAA
Band lengths:
243-393
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: