HsaINT0155814 @ hg19
Intron Retention
Gene
ENSG00000165684 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:11137]
Coordinates
chr9:139275192-139275844:-
Coord C1 exon
chr9:139275774-139275844
Coord A exon
chr9:139275303-139275773
Coord C2 exon
chr9:139275192-139275302
Length
471 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TTGCCTCCTGTGTCCCGCAGCTG
3' ss Score
10.78
Exon sequences
Seq C1 exon
CGGATGGCCTCAGGGAGCAGCTGCAGCAGGCCCGCCTGGCCAGCACCCCTGTGTTTACCCTGTTTACCCAG
Seq A exon
GTAAGCTACTTGGGCAGAGCTTCGTTTTCCTTTGCCTTGTAAAAAGTTTTTGGTGAAGTTTTGAAATCTGCAGTAGATTCATTCCTTAAAGTCTAGCTATCTAAAGTTTTCTAGCCTTGAAAATGCACTTTTCATGCCTTACACTGTTAGCAAGTGAATGTGGAAGGGGTGCCGGCTACAGTGTGCACTGCCCCCATCGGGCTAAACAGTGTCCGGGGAAGGGGGTCCCCGGGGCCCCAGTATGAGTGGAAGATGCCGGGGGAGGAGAGCAGGCCTGGGTCTCATGGGAGGCCATCCTGGATGTCCACAGCCTCATGGCCTCCCCTGCATCTGCATCAGAAGGGCAGGAAGGCTGAGGTCTCAAGGTAGCCGCCCCAGCCTCAGGGCTGCCCCAGGTTCTGCCTAGGCCTCTGGAGCTTCGGAGCTGCTCCCGAAAGCAGCTATGGTTAGGTTGCCTCCTGTGTCCCGCAG
Seq C2 exon
CTGTTCCACATCGATACTGCCGGCTGCTTGGAGGTCGTCCGAGAGAGGAAGGCCCTGCCACCCAGGCTGCCCCAGGCTGGTGCTCGGGACCCACCAGTTCATCTTCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165684-SNAPC4:NM_003086:18
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.250 A=NA C2=0.514
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGATGGCCTCAGGGAGC
R:
CTGCAGAAGATGAACTGGTGGG
Band lengths:
182-653
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)