HsaINT1043525 @ hg38
Intron Retention
Gene
ENSG00000197283 | SYNGAP1
Description
synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497]
Coordinates
chr6:33442889-33444617:+
Coord C1 exon
chr6:33442889-33443960
Coord A exon
chr6:33443961-33444443
Coord C2 exon
chr6:33444444-33444617
Length
483 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
CTCACTGTGCCTTGTCCCAGCAT
3' ss Score
5.96
Exon sequences
Seq C1 exon
CTCTATGGACATGGCTCGCCTCCCCTCCCCAACCAAGGAAAAGCCACCCCCACCACCGCCTGGTGGTGGTAAAGACCTGTTCTATGTAAGCCGTCCACCCCTGGCCCGTTCCTCACCAGCATACTGCACGAGCAGCTCGGACATCACAGAGCCAGAGCAGAAGATGCTGAGTGTCAACAAGAGTGTGTCCATGCTGGACTTACAGGGTGATGGGCCTGGTGGCCGCCTCAACAGCAGCAGTGTTTCGAACCTGGCGGCCGTAGGGGACCTGCTGCACTCAAGCCAGGCCTCGCTGACAGCAGCCTTGGGGCTACGGCCTGCGCCTGCCGGACGCCTCTCCCAGGGGAGTGGCTCATCCATCACGGCGGCTGGCATGCGCCTCAGCCAGATGGGTGTCACCACAGACGGTGTCCCTGCCCAGCAACTGCGAATCCCCCTCTCCTTCCAGAACCCTCTCTTCCACATGGCTGCTGATGGGCCAGGTCCCCCAGGCGGCCATGGAGGGGGCGGTGGCCATGGCCCACCTTCCTCCCATCACCACCACCACCACCATCACCACCACCGAGGTGGAGAGCCCCCTGGGGACACCTTTGCCCCATTCCATGGCTATAGCAAGAGTGAGGACCTCTCTTCCGGGGTCCCCAAGCCCCCTGCTGCCTCCATCCTTCATAGCCACAGCTACAGTGATGAGTTTGGACCCTCTGGCACTGACTTCACCCGTCGGCAGCTTTCACTCCAGGACAACCTGCAGCACATGCTGTCCCCTCCCCAGATCACCATTGGTCCCCAGAGGCCAGCCCCCTCAGGGCCTGGAGGTGGGAGCGGTGGGGGCAGCGGTGGGGGTGGCGGGGGCCAGCCGCCTCCATTGCAGAGGGGCAAGTCTCAGCAGTTGACAGTCAGCGCAGCCCAGAAACCCCGGCCATCCAGCGGGAATCTATTGCAGTCCCCAGAGCCAAGTTATGGCCCCGCCCGTCCACGGCAACAGAGCCTCAGCAAGGAGGGCAGCATTGGGGGCAGCGGGGGCAGCGGTGGCGGAGGGGGTGGGGGGCTGAAGCCCTCCATCACCAAGCAG
Seq A exon
GTAGGTGAAGGCAGGAGGAAGGCGGGCTGGGTCACAACAGGGAGGGAAGAAGGAGATGGGGGGTGGGGTTGAAACAGAGTCTGTGGCCTGAAGTTACAATCTTCTTGCCTCCTTTTGGCCATTAAACAAATGTGTATAGAGGGCCTGCTATGTGCCATGTGCTATGCCAGGCACTAAGGATACGGCACTGAACCCTCTTAGCACTCTCATTCCAGAGGGGATTAATCCATAAGTAGAATGGGGGTGACTGGAATAGGGCCAGCTGGGGGCTTGGAGGCATGAAGATCAGATCCTGAATCAGAACAACAGGAGAAATTCTCTGGCATTCAACTCACATCTCTGGCATTCAGAGGTGATAAAGGCTACAGCAGGGCAATAGGACTGGGACTGTCGTCTCCTTTGGCTGTGCTGTTGCCCTCTAAATGTACCCTGCTTTTTCCCACCTTTTCTTTCTCTGTTCGCCCTCACTGTGCCTTGTCCCAG
Seq C2 exon
CATTCTCAGACACCATCCACATTGAACCCCACAATGCCAGCCTCTGAGCGGACAGTGGCCTGGGTCTCCAACATGCCTCACCTGTCGGCTGACATCGAGAGTGCCCACATCGAGCGGGAAGAGTACAAGCTCAAGGAGTACTCAAAATCGATGGATGAGAGCCGGCTGGATAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197283:ENST00000629380:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.953 A=NA C2=0.972
Domain overlap (PFAM):
C1:
PF120043=DUF3498=PD(22.9=79.2)
A:
NA
C2:
PF120043=DUF3498=FE(10.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCCCAGATCACCATTGGT
R:
TGTGGGGTTCAATGTGGATGG
Band lengths:
342-825
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains