HsaINT0155825 @ hg19
Intron Retention
Gene
ENSG00000165684 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:11137]
Coordinates
chr9:139286394-139287046:-
Coord C1 exon
chr9:139286974-139287046
Coord A exon
chr9:139286559-139286973
Coord C2 exon
chr9:139286394-139286558
Length
415 bp
Sequences
Splice sites
5' ss Seq
AACGTAAGT
5' ss Score
10.74
3' ss Seq
GAGTGTCTCTGTCGGTGCAGTTT
3' ss Score
5.44
Exon sequences
Seq C1 exon
CCAGCTTCCAGAAGAGGCCTTGCTGGGAAACAGGCTGGACAGCCACGACTGGGAGAAGATTTCCAATATTAAC
Seq A exon
GTAAGTCAGGGGCAGGTCTGAGCCCCAAGCAGCTTGGAGCACAGCTCCCTGTAGCCCGGGTGCAGTTGGAATTGGGTGGTAAGGCCACACCCTCCCTGGCAACAGGTTCTGCTGTGACCCCCCACCCACCCGGGTCAAGCACATGTCCCACAGTCGGGAATGGCGAGTGGACTCACGAGGGCCTTCAGGCTGGTGCACGGCCCTTTCTGAGATGGTCTGGAGGGCTCCCGGCCTTGCATCTGGAGCCAAGTCTACATGTTTGGCTATGCAAGGCCTAGTGAGTTGGACGAAGATTGCGCTTACTTGCAGCCGTGGAAGCCTCCAGCTGGCGGAGAGCAACAGCTCAGCCTGGAGCTGCGTCTAGGGTGCCCCTGGGGTCAGTGGCCTGCAAGGCTGAGTGTCTCTGTCGGTGCAG
Seq C2 exon
TTTGAAGGCAGCCGCAGTGCAGAGGAGATCCGGAAGTTCTGGCAGAACTCGGAGCACCCCAGCATCAACAAGCAGGAGTGGAGCAGGGAGGAGGAGGAGCGGCTGCAGGCGATCGCGGCTGCACACGGCCACCTGGAGTGGCAGAAGATTGCAGAGGAGCTGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165684-SNAPC4:NM_003086:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.060 A=NA C2=0.264
Domain overlap (PFAM):
C1:
PF139211=Myb_DNA-bind_6=FE(34.8=100)
A:
NA
C2:
PF139211=Myb_DNA-bind_6=PU(45.9=50.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCCAGAAGAGGCCTTGCTG
R:
CCCAGCTCCTCTGCAATCTTC
Band lengths:
233-648
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)