MmuALTD0003437-3/3 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:106003179-106013446:-
Coord C1 exon
chr9:106013304-106013446
Coord A exon
chr9:106012956-106013303
Coord C2 exon
chr9:106003179-106003269
Length
348 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
GTGTGTATGTGTTGAACTAGGTG
3' ss Score
8.11
Exon sequences
Seq C1 exon
GGAAGGTGGCCGTGTTCTTCCAGGCAGGTAGGAACTATGACACAGCCTCTGTCAGCACAGCCACGTTGGAGCTCCACGCAGCGGACATTGCTACAGCAGTTGTGACCTTCACAGAGGAGCACAACCTCCCAGAGGCAGGGCTG
Seq A exon
GTATGTGAGATGTGGGAAGGGCTGATGGGAGGAGGTGCAAGGGCTGATGGGAGGAGGTGCAAGGGCTGATGGGAAGAGGTTCTGGCGTTAGTCTGGTTTTTACCATTCTACCAGGGATGACATGAGCAGTCAGAGTGGTTCGGGGGAAAAATTCTTCAGAAATTGCTGACTATGGGAGAGGTGAGGGGATCTCAATATGGATACTCTTGACAGAGCTACTACAGATGACCTGGCTCTTAGGAGGCGCATGAATTGTGTAAAGGGCCTCATATCACATGTAATGTACCTAAAGCGCAATTAGTTAGGCCTTGTCGGTTCTCCCTATTGTAAGAAGAAGGCTTAGAGAAG
Seq C2 exon
GTGGATGGACCCAACGAATTTCACCTGTTTACGTGGGAGACCGAGGGCCAGCAGGATGTGGAACGCCTGGCCAGCTGTACTCTCTGCTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032572-50-44,51-44,52-44-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.004 A=NA C2=0.008
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(86.0=93.3)
A:
NA
C2:
PF0009223=VWA=PD(12.8=74.2)
Main Inclusion Isoform:
NA
Other Inclusion 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:
GAAGGTGGCCGTGTTCTTCC
R:
TAGCAGAGAGTACAGCTGGCC
Band lengths:
231-579
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