HsaALTA0001385-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000197768 | C9orf173
Description
chromosome 9 open reading frame 173 [Source:HGNC Symbol;Acc:37285]
Coordinates
chr9:140146889-140147417:+
Coord C1 exon
chr9:140146889-140146977
Coord A exon
chr9:140147114-140147278
Coord C2 exon
chr9:140147279-140147417
Length
165 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGG
5' ss Score
4.94
3' ss Seq
CGTCTCCTACCCCCTCGCAGTGG
3' ss Score
8.32
Exon sequences
Seq C1 exon
AGGGCGGTGGCCGCAGGGCATGGCAGACTTTGTGGTTCCAGAGCGAAAGCCCCTTCACGCAGAAAGCTGACTTCGACCAAGAGCAAAAG
Seq A exon
TGGCCCTCGCCAGCCCACTACCAGCTGCTCAGCCGGCCCGCCTTCCCCGCCTTCAGCTTCAGAGGCTGCCACTCCGCTTCCAAGACACCTGAAGGCCACACCCACCTAGGGCTGCCTGGGGCTAGGGGGCTGGGCCTCAGGGTGCAGCCCCAGTCCCTGCTTCAG
Seq C2 exon
GCCTCTTTGCAGGCACCTGGCAAGAGATGCCCTGGCCCCAACACCTACAATATCCTTCCTGGGAGCCGCCTGCAGAGCCCCCGCTCGCCGGCCTTCTCGATGAGCCGCTCCCCTGCGTTCACCTCCTGGCTCAGCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197768-3-4,3-3-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.422 A=NA C2=0.554
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCATGGCAGACTTTGTGGTT
R:
GTGCTGAGCCAGGAGGTGAA
Band lengths:
210-375
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)