MmuALTD1036948-2/2 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000091345 | Col6a5
Description
collagen, type VI, alpha 5 [Source:MGI Symbol;Acc:MGI:3648134]
Coordinates
chr9:105925760-105928617:-
Coord C1 exon
chr9:105928340-105928617
Coord A exon
chr9:105928042-105928339
Coord C2 exon
chr9:105925760-105926100
Length
298 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
CTCGTTTCTTTGGTCTCCAGATT
3' ss Score
8.28
Exon sequences
Seq C1 exon
CTTGTAACCTTCCGGAAGCTGATGTGATTTTCCTTTGTGATGGCTCTGACATGGTGTCTGATTCAGAGTTCGTTACCATGACAACTTTCTTGTCAGACTTAATTGATAATTTTGACATTGAGTCTCAAAGAATGAAGATTGGGATGGCTCAATACGGGAGCCGGTATCAGGAAATTATTGAGTTGGAAAGCTCTCTGAACAAGACTCAGTGGAAGTCTCAGGTCCACAGTGTGGCCCAGAGCAAGGGGTTGCCACGCCTTGACTTTGCTCTCAAGCAT
Seq A exon
GTGAGTGACATGTTTGATCCATCCGTTGGCGGGAGAAGGAACGCTGGTGTCCCTCAGACTCTGGTTGTTATAACATCTAGTTCTCCACGCTATGATGTGACAGACGCGGTAAAGGTCCTGAAAGACCTTGGCATCTGTGTCCTGGCTTTGGGCATAGGGGATGTTTATAAGGAACAGCTTCTGCCCATCACAGGCAATTCAGAAAAGATAATTACTTTCCGAGACTTTAATAAGCTAAAGAATGTGGATGTGAAGAAGAGAATGGTTCGTGAAATTTGCCAGAGCTGTGGGAAAGCCA
Seq C2 exon
ATTGCTTTGTGGATGTAGTGGTCGGGTTCGACATTTCCACTCACCGTCAGGGCCAGCCTTTGTTCCAGGGCCATCCCCGCTTAGAATCCTACCTCCCGGGCATCTTGGAGGACATCACCTCTATCAGAGGGGTGAGCTGTGGTGCAGGTGCAGAGGCGCAGGTGAGCCTGGCCTTTAAGGTGAACAGTGACCAAGAGTTCCCAGCCAAGTTCCAGATCTATCAGAAAGCAGCGTTTGACAGCTTGTTGCACGTCACAGTCCGTGGACCAACTCATCTGGATGCACCGTTCTTGCAGTCACTTTGGGACATGTTTGAGGAAAGATCTGCATCCAGGGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000091345-12-11,13-11-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=90.2)
A:
NA
C2:
PF057629=VWA_CoxE=PU(43.8=34.2)
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:
CACGCCTTGACTTTGCTCTCA
R:
AGATGAGTTGGTCCACGGACT
Band lengths:
303-601
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