HsaINT0155806 @ hg19
Intron Retention
Gene
ENSG00000165684 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:11137]
Coordinates
chr9:139282194-139283043:-
Coord C1 exon
chr9:139282896-139283043
Coord A exon
chr9:139282301-139282895
Coord C2 exon
chr9:139282194-139282300
Length
595 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGG
5' ss Score
3.71
3' ss Seq
CCCTGTTCCTCTGTCCCTAGTTG
3' ss Score
10.71
Exon sequences
Seq C1 exon
ACCAGCCGCAGCGCCTTCCAGTGCCTGCAGAAATTCCAGCAGCACAACAAAGCTCTGAAACGCAAGGAGTGGACAGAGGAGGAGGACCGCATGCTCACGCAGCTGGTGCAGGAGATGCGCGTCGGCAGCCACATCCCCTACCGCAGAA
Seq A exon
GTGAGGCCCCTCCACCCCGACGGCTCTCAGGCTGTCACAGGGCCCCATATCAGGACACTGGAGACTTGCAGGGAAAATTCACAGAGAAGCAACAAGACAGACGAGGGCTTAGACAGTCCTGGCTGTTCCACAGTTCGCTTCTTGGTGACTCAAGTGACTTTTTTTTTTTTTTTTTTGAGATGGAGTTTCACTCTTGTTGCCCAGGATGGAGTGCAACGCCATGATCTTGGCTCACTGCAACCTCTGCCTCCCGGGTTCAAGCGATTCTCGTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCATGCGCCACCACGCCCAGCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGTCAGGCTGGTCTCGAACTCCTGACCTTAGGTGATCCGCCAGCCTCTGCCTCCCAAAGTGCTGGGATGACAGGCATGATGCCACTGCACCTGGCCAAAGTGATTCTTTTCTATGTGACCCATCTGGAGGGTGGGTGTCTCGGCCCCACGGGACCCTGTTGTCCCTAGCTGTCTACTCTATGGAGGGTGTGTGTCTCGGCCCCACAGGACCTCCCTGTTCCTCTGTCCCTAG
Seq C2 exon
TTGTCTACTATATGGAAGGGAGAGACTCCATGCAGCTGATCTACCGATGGACCAAGAGCTTGGATCCTGGTCTGAAGAAGGGTTACTGGGCCCCGGAGGAAGATGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165684-SNAPC4:NM_003086:10
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=0.000
Domain overlap (PFAM):
C1:
PF139211=Myb_DNA-bind_6=PD(50.8=62.0)
A:
NA
C2:
PF139211=Myb_DNA-bind_6=PU(9.8=16.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCGCCTTCCAGTGCCTG
R:
AGCATCTTCCTCCGGGGC
Band lengths:
246-841
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)