RnoALTA0039500-2/3 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000000483 | Syngap1
Description
synaptic Ras GTPase activating protein 1 [Source:RGD Symbol;Acc:621090]
Coordinates
chr20:5557003-5558635:+
Coord C1 exon
chr20:5557003-5557176
Coord A exon
chr20:5558424-5558429
Coord C2 exon
chr20:5558430-5558635
Length
6 bp
Sequences
Splice sites
5' ss Seq
AGGGTACGC
5' ss Score
8.18
3' ss Seq
GTCGTGTGCCCGGCGGGCAGGTG
3' ss Score
5.41
Exon sequences
Seq C1 exon
CATTCCCAGACTCCATCCACGCTGAACCCCACGATGCCGGCCTCGGAGCGGACTGTAGCCTGGGTGTCCAATATGCCTCACCTGTCCGCTGACATCGAGAGTGCACACATTGAGCGGGAAGAGTACAAGCTGAAGGAGTACTCGAAGTCCATGGACGAGAGCCGACTGGACAGG
Seq A exon
GTGAAG
Seq C2 exon
GAGTACGAGGAGGAGATCCACTCACTGAAGGAAAGGCTACACATGTCCAACCGGAAGCTGGAAGAGTACGAGCGGAGGCTGCTGTCCCAGGAAGAGCAGACCAGCAAGATCCTGATGCAGTACCAAGCCCGCCTGGAGCAGAGCGAGAAGCGCTTGAGGCAGCAGCAGGTGGAGAAGGACTCCCAGATCAAGAGCATCATTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000483-42-44,42-43,42-42-2/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.948 A=NA C2=0.568
Domain overlap (PFAM):
C1:
PF120043=DUF3498=FE(9.8=100)
A:
NA
C2:
PF120043=DUF3498=FE(12.1=100)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
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:
TCGAGAGTGCACACATTGAGC
R:
GTGAGTGGATCTCCTCCTCGT
Band lengths:
105-111
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]