HsaINT0155819 @ hg19
Intron Retention
Gene
ENSG00000165684 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:11137]
Coordinates
chr9:139270029-139270933:-
Coord C1 exon
chr9:139270801-139270933
Coord A exon
chr9:139270253-139270800
Coord C2 exon
chr9:139270029-139270252
Length
548 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CTGGTGTTCCTGTGTTCCAGGAC
3' ss Score
10.97
Exon sequences
Seq C1 exon
GGAGCCCCAGACTCTGGTAAATGCTCTGCTTCCTCCTGCCTGGATACTTCTAATGACCCTGACGACCTGGACGTGCTCAGAACCCGGCATGCCAGGCACACCCGGAAGCGGAGGCGGCTGGTGTGAGCAGCAG
Seq A exon
GTGAGTCCTGAGTGGGGAGGCCACTGCCCTACAACCCAGGGGACAGAGTGGTGTCCAGATGGCAGGGGGCCTTGGCCTCTGCTCGGCTCTTTGGCGCTCACAGCAGGTGTGCTGGGTTAGGTGGGCAGGTCCAGGGTCATGGAGGCCCTCCAGGGGGAGAAGCATTTAACCCACATCCTTCCTGCTGGCCACCCATGCCTCGGGCCTTGGCACCACTGTGCCCCTGACCATAGGCTCATTCCCTGCCTTTGGGGTCTGGGCTCCTCCCTGGCCGCTGTGCTCTGGTGGTGCCCTGTTCCCGTGCATTGCTGCGTCGTCTCCCAGCTTGTAAAACGATCACCATCCCCAACCGCAGCCACCAGGCTGGCTCTTCACTGCTGGAGCCCTGGTGCCCTGGCCTGGCCCTTGGCGCATGTGGGTCAGGTTTACCAAGCAGACTGGGCGTGGCCGGCGCTGGGGTGGTCTTGGTTCCTGTTTGTCTGTCCCAGCCCTGCTTGGGGTCTGGCTGGGGTCAAGGGCACCCCCCACCTGGTGTTCCTGTGTTCCAG
Seq C2 exon
GACAAGCACTTTCTCAGAAGCCCGTGGCCCTGCTGACGAGAGACAGCCCACCCCCAGCCTGCAAGAGAGGCAGCCAGAGGCCAGGTATCTGCTGGCCGCTGACTGACCAGGTCCGCAGTGAACAGAGGCGGGCCTGCCGACTGACTGTGTGGCATGGAGCATGGCTGTTCCCCAAGTGCACACCTGAACACTTGGAGGAATAAAGTTCTGTTTTTAATTGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165684-SNAPC4:NM_003086:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.488 A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGACTCTGGTAAATGCTCTGC
R:
AAAAACAGAACTTTATTCCTCCAAGT
Band lengths:
342-890
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)