HsaINT0146682 @ hg19
Intron Retention
Gene
ENSG00000148396 | SEC16A
Description
SEC16 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:29006]
Coordinates
chr9:139357915-139358192:-
Coord C1 exon
chr9:139358131-139358192
Coord A exon
chr9:139358054-139358130
Coord C2 exon
chr9:139357915-139358053
Length
77 bp
Sequences
Splice sites
5' ss Seq
CAAGTATGT
5' ss Score
7.44
3' ss Seq
ACTGTGTGTTCTTTCTGCAGAGA
3' ss Score
11.39
Exon sequences
Seq C1 exon
GCCTTGCTGCAGCACACGTCTGAGCAGGAGGAGATGCGGGCGTTCCCGGGACCCCTGGCCAA
Seq A exon
GTATGTTCCTTGTTGAGGCATTTCTTTGTGAGCCCGGCCTTGCAGACATCACTGCTCACTGTGTGTTCTTTCTGCAG
Seq C2 exon
AGACGACACCCATAAGGTGGATGTCATTAATTTTGCACAGAACAAAGCTATGAAATGTTTGCAGAATGAAAACTTAATTGACAAAGAGTCTGCAAGTCTTCTTTGGAATTTTATTGTTCTCTTATGCAGACAAAATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148396-SEC16A:NM_014866:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF129322=Sec16=FE(19.4=100)
A:
NA
C2:
PF129322=Sec16=FE(44.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGCAGCACACGTCTGAG
R:
AATTCCAAAGAAGACTTGCAGACTCT
Band lengths:
167-244
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)