HsaINT0155825 @ hg38
Intron Retention
Gene
ENSG00000165684 | SNAPC4
Description
small nuclear RNA activating complex polypeptide 4 [Source:HGNC Symbol;Acc:HGNC:11137]
Coordinates
chr9:136391942-136392594:-
Coord C1 exon
chr9:136392522-136392594
Coord A exon
chr9:136392107-136392521
Coord C2 exon
chr9:136391942-136392106
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:ENST00000298532:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.050 A=NA C2=0.205
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