MmuALTA0004428-2/2 @ mm10
Alternative 3'ss
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:63323919-63324484:+
Coord C1 exon
chr4:63323919-63323981
Coord A exon
chr4:63324394-63324430
Coord C2 exon
chr4:63324431-63324484
Length
37 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
TCTGTCACTCTATTCCCCAGGCC
3' ss Score
9.43
Exon sequences
Seq C1 exon
GGCCCCCCTGGAGACATTGGCTTCAAAGGCATCCAAGGTCCTCGGGGGCCTCCTGGCTTGATG
Seq A exon
GCCCAGATCGAGGACTCATAGCCTCTCTCTCCTTTAG
Seq C2 exon
GGAAAGGAAGGTATCATTGGCCCCCCCGGAATGCTGGGACCTTCTGGACTCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672-83-81,83-80-2/2
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=PU(12.7=38.1)
A:
NA
C2:
PF0139113=Collagen=FE(27.0=100)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCTGGAGACATTGGCTTCA
R:
GGGAGTCCAGAAGGTCCCAG
Band lengths:
112-149
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