HsaINT0155811 @ hg19
Intron Retention
Gene
ENSG00000165684 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:11137]
Coordinates
chr9:139276705-139278120:-
Coord C1 exon
chr9:139277638-139278120
Coord A exon
chr9:139276789-139277637
Coord C2 exon
chr9:139276705-139276788
Length
849 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGC
5' ss Score
8.99
3' ss Seq
TCAGGCAGCTTTCTCATCAGGGT
3' ss Score
3.06
Exon sequences
Seq C1 exon
AAGAAGCAGGGTCTCCGGAGGCGGCGGCGGAGGGCCCGTCACAGCGTCCGGTGGAGCTCTACCAGCAGCAGCGGCAGCAGCAGTGGCAGCAGTGGAGGGAGCAGCAGCAGCAGCAGCAGCAGCAGCGAGGAGGACGAGCCAGAGCAGGCGCAGGCCGGGGAGGGTGACAGAGCGCTGCTGTCCCCACAGTACATGGTCCCGGACATGGACCTGTGGGTTCCTGCCAGGCAGAGCACCAGCCAGCCATGGAGAGGAGGGGCAGGGGCCTGGCTGGGAGGCCCCGCTGCCTCCCTCAGCCCTCCCAAGGGGTCCAGTGCCAGCCAGGGCGGCAGCAAGGAAGCTTCCACCACAGCCGCGGCTCCTGGAGAGGAGACGAGTCCGGTGCAGGTCCCTGCCAGGGCCCACGGCCCTGTCCCGAGGTCTGCCCAGGCCTCCCACTCAGCAGACACTCGCCCGGCGGGCGCAGAGAAGCAGGCCCTGGAG
Seq A exon
GTAGGCCCCGGCCCTGGGTGTACCACGGGAAGTGCACTTTCGGCACTCGCTCGCCAGGGCTGACGCTTGGGGATAGTGCAGCAGCAGGGGCCCCAGGGTTCGTGTGCATCAGAACGTGCTACTTCTGGCTGAGCTCTGGACAGCTGTGCGTCGGGGGGACTGTTGGGGAAGCCTCCATTTTTCCTGGCTTGTTGACTGTTTCAGGGGTATGGCTGAATGGGCACTTGGACCTGGAGGCATTTCTGAAACATTTCACCCCCAAGCCAGGGTTGGGGAGGGCAGAGGCAGCAGTGGGAGGAGCCCCTCCTCCCTCCTCGTGAGCCTGTGCACCTGGAGGCCCTCCCTGGGAAGGGCCTGTCCACCTGCTTGGGACAAGCCTGGCTTGTGGTGTGTCTGCTCGTCTTGGCTGGTCTTCACCGTGTCAGGCCCATCTCTGGCCATGTCTGTGGGAGCAGTCAGAGTTGAACAGGCTGGTCTGTCCTGGGAGTCATTGGCAGGGACAGTGGACACTGAAGCTACTGGCAGAGCTAGGTGCATGGGGCTCGCTGCTGCACAGCCAGCATCTCCCTAGGCCGGGGCGTCACCTGGAAGGGCTGCTGCTGTCAGCCTGAGGAACTGGCTGGGGGGCATGGGACCCTGTTAATGTCCCAGGAGCCAGGCCTAGCTGGGAGGCCCTGCCTGGGGAACCCACGCTTCCCATGGTGGACGTTCCCATGAGGCAGAGCAGAGCTGTACACAGCCACGCTTTGGAGCCTGGGTGAAGAGGCAGTCGTGTGTGGGCAGCGAGGGGAGGGCCCCCATGTGTCCCGTACACCCCGCGTGCCTCGCCTCAGGCAGCTTTCTCATCAG
Seq C2 exon
GGTGGGAGGCGTCTGCTGACAGTGCCTGTGGAGACCGTGCTGAGGGTGCTCAGGGCCAACACGGCTGCTCGGAGCTGCACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165684-SNAPC4:NM_003086:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.981 A=NA C2=0.393
Domain overlap (PFAM):
C1:
PF150891=DUF4552=PD(51.8=36.6)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGTACATGGTCCCGGACAT
R:
CTCAGCACGGTCTCCACAGG
Band lengths:
342-1191
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
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)