MmuALTA0004427-2/2 @ mm10
Alternative 3'ss
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:63317984-63318315:+
Coord C1 exon
chr4:63317984-63318037
Coord A exon
chr4:63318192-63318261
Coord C2 exon
chr4:63318262-63318315
Length
70 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
CCTCACCCGTCCCCCTCCAGGCG
3' ss Score
10.2
Exon sequences
Seq C1 exon
GGTCAAGAGGGAGTTCAAGGCCTCCGTGGAGAACCGGGCCAGCAGGGACAGCCT
Seq A exon
GCGGAGACTGGCCACCCTCCCCAGGAGAGAGGCCTGGAGCTGCCTTGAGTCACCTCACCTTGGTTTGCAG
Seq C2 exon
GGGCATCCAGGACCCCGGGGGCGCCCAGGACCCAAAGGATCAAAAGGCGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672-75-69,75-68-2/2
Average complexity
Alt3
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(27.4=100),PF0139113=Collagen=PU(2.6=11.1)
A:
NA
C2:
PF0139113=Collagen=PD(22.6=77.8),PF0139113=Collagen=FE(21.8=100)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCAAGAGGGAGTTCAAGGCC
R:
TCGCCTTTTGATCCTTTGGGT
Band lengths:
103-173
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