HsaINT0146699 @ hg19
Intron Retention
Gene
ENSG00000148396 | SEC16A
Description
SEC16 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:29006]
Coordinates
chr9:139341679-139342132:-
Coord C1 exon
chr9:139342021-139342132
Coord A exon
chr9:139341817-139342020
Coord C2 exon
chr9:139341679-139341816
Length
204 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TGCTTCCCTCCCCTTTGCAGCAG
3' ss Score
10.57
Exon sequences
Seq C1 exon
AAGAAAGCCCCGCCCCCACCTCCAACCTCGATGCCCAAGACTGTGCAAGCTGCCCCGCCTGCCCTCCCAGGGCCTCCTGGAGCCCCCGTGAACATGTACTCTAGAAGAGCAG
Seq A exon
GTAAGGGTGGCCTTGGAGTGGGAGCTTGCTTGAACGATTAACTGTCCCAGAGAGAGAGGCCAATGTGTAGCTGTTGTGCGTGGGGAGGAGGTGGCTTCCCGCACGTCCCTGCGTGCTTTTCCTCTGACGCAGTGAGCGCAGAGCATTTGGAAGCTGGAGGCCACCTGGCGCGTTCACCTCAATTTGCTTCCCTCCCCTTTGCAG
Seq C2 exon
CAGGAACCAGAGCTCGCTACGTTGACGTCCTGAACCCAAGCGGGACCCAGCGGAGCGAGCCGGCTCTCGCTCCTGCGGACTTTGTCGCTCCACTCGCGCCACTCCCAATTCCTTCTAACTTGTTCGTGCCAACCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148396-SEC16A:NM_014866:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.973 A=NA C2=0.898
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CCCCACCTCCAACCTCGAT
R:
CTGGGGTTGGCACGAACAAG
Band lengths:
237-441
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)