HsaINT0155810 @ hg19
Intron Retention
Gene
ENSG00000165684 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:11137]
Coordinates
chr9:139277638-139278484:-
Coord C1 exon
chr9:139278405-139278484
Coord A exon
chr9:139278121-139278404
Coord C2 exon
chr9:139277638-139278120
Length
284 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGC
5' ss Score
5.97
3' ss Seq
TAGCTCTTTCCTCCCCTCAGAAG
3' ss Score
7.41
Exon sequences
Seq C1 exon
GTCACTGGGCAAAAATAGCTTCTGAGCTGCCCCATCGGTCTGGCTCCCAGTGTCTGAGCAAGTGGAAGATCATGATGGGG
Seq A exon
GTGAGCCACTCGCTCCTTCTTTATCTGAAACCAGACAATGGCCTGGTCAACTGGGGGGTCCAGCAGGCAGGAGGAGGGGAGGGGAGGGGGGCGTTCGGTTTCTGGTCTTGGCATTTCTTCTTCTGGGTGGCCAAGGGCAAAGGGAGACCCTGCCTCGGCAGCGGCTGCTCTTGACCCCGGAGGCGCCCCCGCTTGGGCCTCTCCCCAAAGGGCTGGCCTGCTTGCTGCCATCATGGGTGAACCGGGCTTGCCAAGGCCTCTAAGTAGCTCTTTCCTCCCCTCAG
Seq C2 exon
AAGAAGCAGGGTCTCCGGAGGCGGCGGCGGAGGGCCCGTCACAGCGTCCGGTGGAGCTCTACCAGCAGCAGCGGCAGCAGCAGTGGCAGCAGTGGAGGGAGCAGCAGCAGCAGCAGCAGCAGCAGCGAGGAGGACGAGCCAGAGCAGGCGCAGGCCGGGGAGGGTGACAGAGCGCTGCTGTCCCCACAGTACATGGTCCCGGACATGGACCTGTGGGTTCCTGCCAGGCAGAGCACCAGCCAGCCATGGAGAGGAGGGGCAGGGGCCTGGCTGGGAGGCCCCGCTGCCTCCCTCAGCCCTCCCAAGGGGTCCAGTGCCAGCCAGGGCGGCAGCAAGGAAGCTTCCACCACAGCCGCGGCTCCTGGAGAGGAGACGAGTCCGGTGCAGGTCCCTGCCAGGGCCCACGGCCCTGTCCCGAGGTCTGCCCAGGCCTCCCACTCAGCAGACACTCGCCCGGCGGGCGCAGAGAAGCAGGCCCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165684-SNAPC4:NM_003086:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.981
Domain overlap (PFAM):
C1:
PF150891=DUF4552=FE(22.8=100)
A:
NA
C2:
PF150891=DUF4552=PD(51.8=36.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCCAGTGTCTGAGCAAGTG
R:
CTCCTCTCCATGGCTGGCT
Band lengths:
293-577
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
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)