RnoINT0146743 @ rn6
Intron Retention
Gene
ENSRNOG00000000483 | Syngap1
Description
synaptic Ras GTPase activating protein 1 [Source:RGD Symbol;Acc:621090]
Coordinates
chr20:5548630-5549084:+
Coord C1 exon
chr20:5548630-5548783
Coord A exon
chr20:5548784-5548985
Coord C2 exon
chr20:5548986-5549084
Length
202 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGTG
5' ss Score
4.58
3' ss Seq
AAATCCACACTCCTCTCCAGGTA
3' ss Score
5.43
Exon sequences
Seq C1 exon
GGCCCGGCTGATGCAGAGCTTCAAGGAGTCTCACTCCCATGAGTCCCTGCTGAGTCCCAGCAGTGCTGCTGAGGCCCTGGAGCTCAACCTGGATGAAGACTCCATTATCAAGCCAGTACACAGCTCCATCCTGGGCCAGGAGTTCTGCTTTGAG
Seq A exon
GTAGTGGCTTTGAGGGCTGCTGTGGACTGAGAGGCAGGGATGCAGGAGGGTAGGGGCCCCCGAGGGCCTTGAGTAAGTGGCATATTCGGGGATGTCAGGGGAACAGGGCTGGGATAAGGAAGGAAGGCGTGGTGTGGTCTTTGGCCTCTAGGAGGCACGCTTCTCCCGTGGGGCCCCATCTCAAATCCACACTCCTCTCCAG
Seq C2 exon
GTAACAACATCGTCTGGGACAAAATGTTTTGCCTGTCGGTCTGCAGCCGAAAGGGACAAATGGATTGAGAATCTACAGAGGGCTGTGAAACCCAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000483:ENSRNOT00000000572:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.231 A=NA C2=0.121
Domain overlap (PFAM):
C1:
PF0016924=PH=FE(23.1=100)
A:
NA
C2:
PF0016924=PH=PD(13.1=87.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGATGCAGAGCTTCAAGGA
R:
TTGTTGGGTTTCACAGCCCTC
Band lengths:
246-448
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]