RnoINT0146741 @ rn6
Intron Retention
Gene
ENSRNOG00000000483 | Syngap1
Description
synaptic Ras GTPase activating protein 1 [Source:RGD Symbol;Acc:621090]
Coordinates
chr20:5546577-5547158:+
Coord C1 exon
chr20:5546577-5546668
Coord A exon
chr20:5546669-5547036
Coord C2 exon
chr20:5547037-5547158
Length
368 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
ATTTCCCATTTGCTCCCCAGCAA
3' ss Score
6.93
Exon sequences
Seq C1 exon
AATACCACTTGGGTCGCTCGAGGAGGAAGAGTGTCCCCGGGGGGAAACAGTACAGCATGGAAGCCGCCCCCGCTGCGCCCTTCCGGCCCTCG
Seq A exon
GTGAGTGAATGAAGTGGCTGCCAGATGTGGCTCAGCCTGGCCCCTCCAGCCCCAGCGGGAGCTCCAGGATTCTGAAAAAGAGGGCCCAGGGAAGAGTGTGCATGTATTCCCCACCTCTTTGGTTTACCCCTTCTTGGCTCTGCCCCCTACTTCTTGGACCAGCCCTCCCACCTTTTCCAAGCGAGTGTGTGTGTTTGTGTATCTGCTCACATCAGACAGTACCCGTGGGAGCAAGGAAGACAAACTGGTGTCAGGGCTCTTGTCCCTTTTCCTCTGCTCCACGTTCTTCCAGGGCTTCCCTGCCAGCTCAGGGTGTCTAGGGAGAGACTGAGCTGCCCCAAGCACCCCATTTCCCATTTGCTCCCCAG
Seq C2 exon
CAAGGCTTCCTGAGCCGGAGGCTAAAAAGCTCCATCAAACGTACAAAGTCACAACCCAAACTTGACCGGACCAGCAGCTTTCGACAGATCCTGCCTCGCTTCCGAAGTGCTGACCATGACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000483:ENSRNOT00000000572:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.774 A=NA C2=0.341
Domain overlap (PFAM):
C1:
PF0016924=PH=FE(13.6=100)
A:
NA
C2:
PF0016924=PH=FE(18.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTTGGGTCGCTCGAGGAG
R:
GTCATGGTCAGCACTTCGGAA
Band lengths:
206-574
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]