HsaALTA0007946-3/3 @ hg19
Alternative 3'ss
Gene
ENSG00000080189 | SLC35C2
Description
solute carrier family 35, member C2 [Source:HGNC Symbol;Acc:17117]
Coordinates
chr20:44983743-44984513:-
Coord C1 exon
chr20:44984441-44984513
Coord A exon
chr20:44983818-44983918
Coord C2 exon
chr20:44983743-44983817
Length
101 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
ATGAACCCTTGACCCTCAAGACC
3' ss Score
2.75
Exon sequences
Seq C1 exon
GTACACAATGACCAAATCCTCAGCTGTCCTCTTCATCTTGATCTTCTCTCTGATCTTCAAGCTGGAGGAGCTG
Seq A exon
ACCCCCGAGTTAGCTGCCACTGCTCCCCATCCTACCAGCGCGCGGCACTGGTCCTGGTGGTCCTCCTCATCGCCGGGGGTCTCTTCATGTTCACCTACAAG
Seq C2 exon
TCCACACAGTTCAACGTGGAGGGCTTCGCCTTGGTGCTGGGGGCCTCGTTCATCGGTGGCATTCGCTGGACCCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080189-9-16,9-14,9-13-3/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0089215=EamA=FE(16.4=100)
A:
NA
C2:
PF0315111=TPT=PU(18.5=77.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
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:
ACACAATGACCAAATCCTCAGCT
R:
GAGGGTCCAGCGAATGCCA
Band lengths:
146-247
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)