MmuALTD0003423-1/3 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:63258152-63263772:+
Coord C1 exon
chr4:63258152-63258188
Coord A exon
NA
Coord C2 exon
chr4:63263719-63263772
Length
0 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGC
5' ss Score
6.03
3' ss Seq
CTTCTCTCTCATCCCCTCAGGGC
3' ss Score
12.07
Exon sequences
Seq C1 exon
GGTCTCCCTGGCGTTCCTGGCAAGAGGGGCGAGATGG
Seq A exon
NA
Seq C2 exon
GGCTTCCCTGGAGACTTTGGGGAAAGAGGCCCCCCTGGACTTGATGGCAACCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672-25-21,26-21,27-21-1/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence exclusion)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(14.9=100),PF0139113=Collagen=FE(15.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(9.6=50.0),PF0139113=Collagen=FE(18.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGCGTTCCTGGCAAGAG
R:
AGGGTTGCCATCAAGTCCAGG
Band lengths:
84-92
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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