MmuALTD0003406-1/2 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000040690 | Col16a1
Description
collagen, type XVI, alpha 1 [Source:MGI Symbol;Acc:MGI:1095396]
Coordinates
chr4:130081435-130083175:+
Coord C1 exon
chr4:130081435-130081479
Coord A exon
NA
Coord C2 exon
chr4:130083122-130083175
Length
0 bp
Sequences
Splice sites
5' ss Seq
CCCGTAAGA
5' ss Score
5.66
3' ss Seq
TCATGGTTTCTCTCTCTAAGGGG
3' ss Score
7.32
Exon sequences
Seq C1 exon
GGCCCCCCAGGTTTTCCTGGTGCTGTTGGCTCCCCCGGATTGCCC
Seq A exon
NA
Seq C2 exon
GGGCTTCAAGGGGAGCGAGGCCTCACGGGCCTGACTGGAGACAAAGGAGAACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040690-74-86,76-86-1/2
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(22.6=100),PF0139113=Collagen=PU(19.2=93.3)
A:
NA
C2:
PF0139113=Collagen=FE(27.0=100),PF0139113=Collagen=FE(23.9=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:
GTTTTCCTGGTGCTGTTGGCT
R:
CTCCTTTGTCTCCAGTCAGGC
Band lengths:
84-126
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