DreINT0020562 @ danRer10
Intron Retention
Gene
ENSDARG00000069765 | SYNGAP1 (2 of 2)
Description
synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497]
Coordinates
chr16:45662278-45663718:+
Coord C1 exon
chr16:45662278-45662422
Coord A exon
chr16:45662423-45663481
Coord C2 exon
chr16:45663482-45663718
Length
1059 bp
Sequences
Splice sites
5' ss Seq
TTGGTCAGT
5' ss Score
5.07
3' ss Seq
TTAATTTGATGTGTTTTCAGTGC
3' ss Score
7.11
Exon sequences
Seq C1 exon
GTGATTTTATCCGAGCGCTGTATGAATCAGAGGAGAACTGTGAAGTGGACCCGATGCGAACTCCCCCTTCAATACTGCCCGAACATCAAGCCAACCTCCGGATGTGCTGTGAGCTCGCCCTCTGCAAAATCATCAACTCATATTG
Seq A exon
GTCAGTTTTATTGATTTTGAATCAACACATTCGTTTAAAAATGATTGAGTTGTGCAAAATAATCCTGAAAAAAGCTGCAGGATGCATTGAAGCAGGCTGATATATCAAAGTAGGGCACTTTTGTTTTGCACAGTTATTTATAAATAACGTTTATATATGATTGGTGTCATTAAGTGCGCCACACAACAGGGCTATATAATGGTGTTTAAAAATTGATTTATTTTTACGTTTTTGTCTTACATTTTACTGCTAATTGTATTATTCTATTACTTTTTAAATCAGTTTAAAAGGCTCTTTTGATGATAGTCATAAGTTTTTTTTATCTGATATTAAGTGCAGATGAAAATAATATAATGAGACTCATTATTGATTCATTTATTTGTTTATTTTAAATAATTTACTTATTTATTTATTTAATTATTTGATATGGGTTTTGCCTATTAATAGTTTTTGCTTTGTGATTTAATTTAAATATATACAGGAGTTACAATACAATACAATACAATAAAACCTGGTTTTAGAACCCAATAATTCATTAGTATGGTGTAGGTCCTTCTTTTGTGGCCAATACAGCATCATGTCATCTTGGGAATGACATATACAAGTCCTTACAGTGATCAGAGGGATTTTGAGCTATTCTTCTTGCAGAATAGTGGCCGGGACACTGCATGATGCTGGTGGAGAAAAACATTTCCTGACTCGCTCCTCCAAAATACCCTAAAGTAGCTCAATAATATTTAGATCTGGTGACTGTGCTGGCCATGGGAGATGTTCAACTTCTATAAACTGTAAATAGTCACATTAATCTTTCACCGGGAGATTGAAACACTTCTGTGCATATAACCCATTCATAACAACACAATCTACATCAGCTCTGTGTGACTGAAATAGTTTTAAAACAGAACATAACCTGTCTAATAGAAATACTTCAGCCATGGCGTCGTTCTTCCTCCAGCATGCAAAAGTAGCTCCAATATTGATTCAGGGTTTTAAAGTTTTGTCTGATGCTCTCAATCTTCATGAGTGTGAATGGTAATGTTTAATTTGATGTGTTTTCAG
Seq C2 exon
TGCGTTCCCGCGAGAGCTGAAGGAAGTGTTTGCATCATGGCGTGTCCGCTGTGCTGAGAGAGGAAGAGAAGACATTGCAGATCGACTGATCAGCGGCTCCCTCTTCCTGCGCTTCCTCTGTCCAGCCATCATGTCTCCATCTCTGTTCAACCTCACGCAGGAATATCCCGATGAGCAGACCTCACGAACACTCACACTCATCGCCAAAGTGGTCCAGAACCTCGCAAACTTCTCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069765:ENSDART00000143867:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.041 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061614=RasGAP=FE(27.9=100)
A:
NA
C2:
PF0061614=RasGAP=PD(44.2=95.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGAGCGCTGTATGAATCAGA
R:
GTTCTGGACCACTTTGGCGAT
Band lengths:
355-1414
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]