HsaINT0146686 @ hg19
Intron Retention
Gene
ENSG00000148396 | SEC16A
Description
SEC16 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:29006]
Coordinates
chr9:139354209-139354575:-
Coord C1 exon
chr9:139354494-139354575
Coord A exon
chr9:139354327-139354493
Coord C2 exon
chr9:139354209-139354326
Length
167 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
TTTGTTTTTCCTCATGTTAGTGC
3' ss Score
7.25
Exon sequences
Seq C1 exon
GTTTGCTAACAGCCTCCCAATCAACGACCCTCTGCAGACAGTCTACCAGCTCATGTCCGGACGGATGCCTGCCGCGTCCACG
Seq A exon
GTGAGTGGCACTGCCTGGTGGCTTGCACAGGCTCCACTGCCTGTGTGGAGTTTGCTCGTGGGTGACGCTGTCACAGGCCGTGAGGTGCCTGGTGAGCCCAGCTGTGTGGAATTGAAATGGCGCTGGCTTCCGGGGATGAGGCTTCGTTTTGTTTTTCCTCATGTTAG
Seq C2 exon
TGCTGTGGAGACGAGAAATGGGGAGATTGGAGGCCGCACCTCGCCATGGTCTTGTCCAACTTGAACAACAACATGGACGTCGAGTCCAGGACGATGGCTACCATGGGCGACACTCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148396-SEC16A:NM_014866:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF129312=Sec16_C=FE(10.3=100)
A:
NA
C2:
PF129312=Sec16_C=FE(14.9=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:
TGCTAACAGCCTCCCAATCAAC
R:
CCAGAGTGTCGCCCATGGTAG
Band lengths:
197-364
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)