MmuALTD0003425-1/2 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:63293201-63293523:+
Coord C1 exon
chr4:63293201-63293254
Coord A exon
NA
Coord C2 exon
chr4:63293470-63293523
Length
0 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
TTTTTCTTCCTCCTTGGCAGGGC
3' ss Score
10.02
Exon sequences
Seq C1 exon
GGAGACCGTGGGGTGATGGGACCCCCAGGTGCACCTGGACCCAAGGGGTCGATG
Seq A exon
NA
Seq C2 exon
GGCCATCCTGGAACACCCGGTGGTATTGGGAACCCTGGAGAGCCTGGACCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672-45-39,46-39-1/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
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=FE(20.7=100),PF0139113=Collagen=PU(20.7=94.4)
Main Skipping Isoform:
NA
Other Skipping 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
- 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