HsaALTA0007563-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000120341 | SEC16B
Description
Protein transport protein Sec16B [Source:UniProtKB/Swiss-Prot;Acc:Q96JE7]
Coordinates
chr1:177929926-177930869:-
Coord C1 exon
chr1:177930725-177930869
Coord A exon
chr1:177930075-177930077
Coord C2 exon
chr1:177929926-177930074
Length
3 bp
Sequences
Splice sites
5' ss Seq
CTGGTGGGT
5' ss Score
6.29
3' ss Seq
CATCTGTGTCTGTTGGTCAGAAG
3' ss Score
3.55
Exon sequences
Seq C1 exon
CCATCATTGGCTAGTGAGTCCAACCTTCTCCAGCAGCGTGAGTCTGGTCTCAGCTCCAGCAGCTATGAGCTCAGTCAGTACATCAGAGATGCCCCGGAGCGGGATGATCCCCCAGCTTCAGCAGCTTGGAGTCCAGTTCAGGCTG
Seq A exon
AAG
Seq C2 exon
ATGTCTCCTCAGCTGGTCCCAAAGCACCCATGAAGTTCTACATCCCTCATGTTCCTGTGAGTTTCGGGCCAGGAGGTCAGCTGGTGCATGTAGGTCCCAGCTCTCCCACTGACGGGCAAGCAGCCCTTGTTGAACTGCACAGCATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120341-27-29,27-28-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.883 A=NA C2=0.379
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF129322=Sec16=PU(33.3=68.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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:
CTTCAGCAGCTTGGAGTCCAG
R:
GCCCGAAACTCACAGGAACAT
Band lengths:
99-102
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)