HsaINT1043522 @ hg38
Intron Retention
Gene
ENSG00000197283 | SYNGAP1
Description
synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497]
Coordinates
chr6:33441173-33441759:+
Coord C1 exon
chr6:33441173-33441374
Coord A exon
chr6:33441375-33441580
Coord C2 exon
chr6:33441581-33441759
Length
206 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGC
5' ss Score
7.09
3' ss Seq
TAACAGCCTCACCCTTCCAGGAA
3' ss Score
6.95
Exon sequences
Seq C1 exon
GTTTACCTCAAAGGAGGACTTTCTGGGCTTCATGAATGAGTTTCTGGAGCTGGAATGGGGTTCCATGCAGCAGTTTTTGTATGAGATCTCCAATCTGGACACGCTAACCAACAGCAGTAGCTTTGAGGGTTACATCGACTTGGGCCGAGAGCTCTCCACACTGCATGCCCTACTCTGGGAGGTGCTGCCCCAGCTCAGCAAG
Seq A exon
GTCAGCAGATCCCCTCTTTGCCCTATCCCCAGATGGCTCCAGAGGTTCCTGGAGCCTGAGAAACTACCCTTTGAAGATTTTTTTTCTCCCCTTGTTTCTCGAGGTGTCACCACTACTATCCCAACTCAGGCCCCCTCCACCTGCACCCTCAGAGGCCCTCTTAGAGCTGGGCACTGAGCCCCCAGGTAACAGCCTCACCCTTCCAG
Seq C2 exon
GAAGCCCTCCTGAAGCTGGGTCCACTGCCCCGGCTCCTCAACGACATCAGCACAGCTCTGAGGAACCCCAACATCCAAAGGCAGCCAAGCCGCCAGAGTGAGCGGCCCCGGCCTCAGCCTGTGGTACTGCGGGGGCCATCGGCTGAGATGCAGGGCTACATGATGCGGGACCTCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197283:ENST00000629380:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.570
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF120043=DUF3498=PU(56.6=78.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGGTTCCATGCAGCAGTTTT
R:
CATGTAGCCCTGCATCTCAGC
Band lengths:
308-514
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains