MmuALTD1026547-1/3 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000040690 | Col16a1
Description
collagen, type XVI, alpha 1 [Source:MGI Symbol;Acc:MGI:1095396]
Coordinates
chr4:130060874-130061380:+
Coord C1 exon
chr4:130060874-130060984
Coord A exon
NA
Coord C2 exon
chr4:130061345-130061380
Length
0 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TCATATACCCTCTCTTTCAGGAG
3' ss Score
10.05
Exon sequences
Seq C1 exon
GGTGACCCCTGTGAAGTGTGCCCAACGCTGCCTGAAGGGTCCCAGAATTTTGTGGGGCTCCCTGGAAAACCAGGGCCTAAAGGGGAACCAGGTGATCCTGCTCCAGCCTGG
Seq A exon
NA
Seq C2 exon
GAGGGCCTAGGAACTGTGGGACTGAAAGGTGACCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040690-36-38,37-38,38-38-1/3
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=PD(14.3=21.6),PF0139113=Collagen=PU(41.3=70.3)
A:
NA
C2:
PF0139113=Collagen=FE(17.5=100)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
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:
GTGACCCCTGTGAAGTGTGC
R:
GGTCACCTTTCAGTCCCACAG
Band lengths:
144-360
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