HsaINT0155805 @ hg19
Intron Retention
Gene
ENSG00000165684 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:11137]
Coordinates
chr9:139291429-139292889:-
Coord C1 exon
chr9:139292751-139292889
Coord A exon
chr9:139291476-139292750
Coord C2 exon
chr9:139291429-139291475
Length
1275 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
GTTGCTTGTGTTTCTGACAGATT
3' ss Score
8.79
Exon sequences
Seq C1 exon
GCGGGAGTCATGGATGTAGATGCTGAAAGAGAGAAGATAACACAGGAGATCAAGGAGCTGGAAAGGATTTTGGATCCCGGCTCCTCGGGCTCCCACGTGGAGATCTCAGAATCAAGTCTCGAGTCAGATTCTGAAGCAG
Seq A exon
GTAAGCCCCTTGTACCTAGCCTCCTGGGGTCCTGGTAAGAACAGCTGGTCTGCCTCCTGGGTTCCTCTCAGGCACATTAGGGAGTGATGGTAGCCGGGTGTGGTTTCTCAGGCCTGTAAACCCAGGGACTCCTGAGGCTGAGGTGAGAGCATTGTTTGATCCCAGGAGTTCATGTCCAGCCTGGACAACGCAGCAAGACCCTGTCTCTAAAAATAATAATAATAATAATAAACGATGGCTGGTGCTGCTTGGACCAGACCCAATTTTTTGCCAACACTGGTGTCTTTCTGTACTCCAGCCAGAGAGCTTCTGACAATTCCTCCTTTGCTAGCCCCTGAACCAGCTGGCTGTGTGTGTACACTGGGCTCTAGGCATCCCAGGGTCTGGGCCTGGCCTCCTTGGGCCTGTGCAGGGCTTCTGGAGTGGACCATCCTGGGAGGAGGGGGCAGGCCTGAACCTCACCAGATGGCAGTCTGGACAGTCCATGCCTGGATGGTCAACACAGCTCACACCCCTAGGATCTCTTCTTCTCACATGTGCCCCTCCCCACGTGCTCCCCACCCCAAGTGCTCTCCTCCCCACGTGCTCCCCACCCCACGTGCTCCCCACCCCACGTGCTCCCCTCCCCACGTGCTCCCCTCCCCACGTGCTCCCCTCCCCACGTGCTCCCCACCCCACGTGCTCCCCTCCCCATGTGCTCCCCACCCCATAGGCTCCCCACCCCACAGCCTCTCCTCCCAACATGCTCCCCTCCCCACATGCTCTCCTCCATGCTCCCTTTAGCTTCTGAGCCTACCCCAACCCCACCAGCTGCTGCCCTGACAGGAGACCCCCCCAGCCTTGCTTCCCACCTCTCCCAGACCCAGGGCCTGCCTCTGAGGCAACCTGCTATCTTTCTCCTGTGGTGAGGGCCTCTACATCCGTGCCTCCCATCTGACCGGCTAAGCTCCTGAAGGAGAGGTCCGTTTTCTGCTAAACTTTCCCTGTCTCTCCAGTAAAGATAGCTTGTGCCATCCAGTGAACCCTGTGTAGCTTTGTCCTGTGTGCCTGGAGGTCCCCAGTGTGTGGTCAGAGTTTTCTCTATCTGGCTAACCCGGCCTTGGTCCAGTGCCCACCCCGCTGTCAGGGAGGGAAGGTCCGCTCACCGCCAGCCTCAGCCTGAGGCGCTGTCACTACCTCACAACCCCAGGTCTGCCCAAGAAGCAGTGGTGAGCTGCGCCCCCACCCTGCCCAAGACGCTGGTTACCAACACGGTGTTGCTTGTGTTTCTGACAG
Seq C2 exon
ATTCACTGCCTTCTGAGGACTTGGATCCTGCCGATCCCCCGATCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165684-SNAPC4:NM_003086:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion 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:
CGGGAGTCATGGATGTAGATGC
R:
GAGATCGGGGGATCGGCAG
Band lengths:
184-1459
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)