HsaALTA0002054-2/2 @ hg38
Alternative 3'ss
Gene
ENSG00000163359 | COL6A3
Description
collagen type VI alpha 3 chain [Source:HGNC Symbol;Acc:HGNC:2213]
Coordinates
chr2:237339015-237341150:-
Coord C1 exon
chr2:237340452-237341150
Coord A exon
chr2:237339091-237339117
Coord C2 exon
chr2:237339015-237339090
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
ATATCAGGAAACAGTGTGATTGGTTCCAAGGGGACCAACCCACAAAGAACCTTGTGAAGTTTGGTCACAAACAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163359-73-82,73-81-2/2
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 Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
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