HsaALTA1053489-2/2 @ hg38
Alternative 3'ss
Gene
ENSG00000196739 | COL27A1
Description
collagen type XXVII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:22986]
Coordinates
chr9:114304608-114306688:+
Coord C1 exon
chr9:114304608-114304673
Coord A exon
chr9:114306520-114306521
Coord C2 exon
chr9:114306522-114306688
Length
2 bp
Sequences
Splice sites
5' ss Seq
GAGGTATCT
5' ss Score
7.27
3' ss Seq
CCACCCTCTCCTCGTGACAGAGT
3' ss Score
7.66
Exon sequences
Seq C1 exon
CAACAAGATGATCTTGGGGCAGCTTTCCAGACGTGGATGGACACCAGTGGAGCACTCAGGCCAGAG
Seq A exon
AG
Seq C2 exon
TTACAGCTATCCAGACCGGCTGGTGCTGGACCAGGGAGGAGAGATCTTTAAAACCTTACACTACCTCAGCAACCTCATCCAGAGCATTAAGACGCCCCTGGGCACCAAAGAGAACCCCGCCCGGGTCTGCAGGGACCTCATGGACTGTGAGCAGAAGATGGTGGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196739-101-109,101-108-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.782 A=NA C2=0.225
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0141013=COLFI=PU(39.1=47.4)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATCTTGGGGCAGCTTTCCAG
R:
AGATCTCTCCTCCCTGGTCCA
Band lengths:
104-106
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains