HsaALTA0002054-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000163359 | COL6A3
Description
collagen, type VI, alpha 3 [Source:HGNC Symbol;Acc:2213]
Coordinates
chr2:238247660-238249793:-
Coord C1 exon
chr2:238249095-238249793
Coord A exon
chr2:238247734-238247760
Coord C2 exon
chr2:238247660-238247733
Length
27 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
TCTTTGTTTTTTTTCTTTAGGTG
3' ss Score
12.54
Exon sequences
Seq C1 exon
CAAGGCCTCCCAGCACTTCGCCAGAGTGGCAGTTGTGCAGCACGCGCCCTCTGAGTCCGTGGACAATGCCAGCATGCCACCTGTGAAGGTGGAATTCTCCCTGACTGACTATGGCTCCAAGGAGAAGCTGGTGGACTTCCTCAGCAGGGGAATGACACAGTTGCAGGGAACCAGGGCCTTAGGCAGTGCCATTGAATACACCATAGAGAATGTCTTTGAAAGTGCCCCAAACCCACGGGACCTGAAAATTGTGGTCCTGATGCTGACGGGCGAGGTGCCGGAGCAGCAGCTGGAGGAGGCCCAGAGAGTCATCCTGCAGGCCAAATGCAAGGGCTACTTCTTCGTGGTCCTGGGCATTGGCAGGAAGGTGAACATCAAGGAGGTATACACCTTCGCCAGTGAGCCAAACGACGTCTTCTTCAAATTAGTGGACAAGTCCACCGAGCTCAACGAGGAGCCTTTGATGCGCTTCGGGAGGCTGTTGCCATCCTTCGTCAGCA
Seq A exon
GTGAAAATGCTTTTTACTTGTCCCCAG
Seq C2 exon
ATATCAGGAAACAGTGTGATTGGTTCCAAGGGGACCAACCCACAAAGAACCTTGTGAAGTTTGGTCACAAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163359-49-56,49-55-2/2
Average complexity
Alt3
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=0.171
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=82.1)
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACAAGTCCACCGAGCTCAAC
R:
AGGTTCTTTGTGGGTTGGTCC
Band lengths:
122-149
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)