RnoALTA0039498-4/4 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000000483 | Syngap1
Description
synaptic Ras GTPase activating protein 1 [Source:RGD Symbol;Acc:621090]
Coordinates
chr20:5551998-5553748:+
Coord C1 exon
chr20:5551998-5552142
Coord A exon
chr20:5553366-5553540
Coord C2 exon
chr20:5553541-5553748
Length
175 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGA
5' ss Score
6.29
3' ss Seq
CCCGTGGCCCTCTTCTTCAGCAG
3' ss Score
7.22
Exon sequences
Seq C1 exon
GGGAGTTCATCCGGGCTCTGTATGAATCTGAGGAGAACTGTGAAGTAGACCCCATCAAGTGCACAGCGTCCAGTCTGGCAGAGCACCAGGCCAACCTGCGGATGTGCTGTGAGTTGGCCCTGTGCAAGGTGGTCAACTCCCATTG
Seq A exon
CAGCCTCCTGTCTTTCTCCTGCAGTCCCTCCCTCCTGGTCTCTCACCTGTCTCCACACCTCCTCTCACCTCCTACCACCCCTCAGCATGTTCCCTGAAGGCTGAGGGTCTCTGGGGCTCAGTCCCGGTCTCTCTTTCTCTCTCTCTCTCTCTGTCTCCCCACCCCTTCCCCTCAG
Seq C2 exon
CGTGTTCCCGGGGGAGCTGAAGGAGGTGTTTGCATCATGGCGGCTGCGCTGTGCAGAGCGGGGCCGGGAGGACATTGCTGACAGGCTGATCAGCGCCTCGCTCTTCCTGCGCTTCCTCTGCCCGGCCATCATGTCGCCCAGTCTGTTTGGACTGATGCAGGAGTACCCAGATGAGCAGACCTCACGAACCCTCACCCTCATCGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000483-31-32,31-31,31-30,31-29-4/4
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 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
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTAGACCCCATCAAGTGCACA
R:
CAAACAGACTGGGCGACATGA
Band lengths:
250-425
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]