MmuALTA0004428-2/2 @ mm9
Alternative 3'ss
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:62984953-62985518:+
Coord C1 exon
chr4:62984953-62985015
Coord A exon
chr4:62985428-62985464
Coord C2 exon
chr4:62985465-62985518
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
ENSMUSG00000045672-59-60,59-59-2/2
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)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
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
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: