MmuALTD0003425-2/2 @ mm9
Alternative 5'ss
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:62954235-62954557:+
Coord C1 exon
chr4:62954235-62954288
Coord A exon
chr4:62954289-62954295
Coord C2 exon
chr4:62954504-62954557
Length
7 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGT
5' ss Score
8.57
3' ss Seq
TTTTTCTTCCTCCTTGGCAGGGC
3' ss Score
10.02
Exon sequences
Seq C1 exon
GGAGACCGTGGGGTGATGGGACCCCCAGGTGCACCTGGACCCAAGGGGTCGATG
Seq A exon
GTAAGGA
Seq C2 exon
GGCCATCCTGGAACACCCGGTGGTATTGGGAACCCTGGAGAGCCTGGACCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672-32-31,33-31-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(19.3=100),PF0139113=Collagen=FE(27.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(6.8=33.3),PF0139113=Collagen=FE(27.9=100)
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:
CCGTGGGGTGATGGGACC
R:
GGCTCTCCAGGGTTCCCAATA
Band lengths:
93-100
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: