RnoINT0146731 @ rn6
Intron Retention
Gene
ENSRNOG00000000483 | Syngap1
Description
synaptic Ras GTPase activating protein 1 [Source:RGD Symbol;Acc:621090]
Coordinates
chr20:5553863-5554451:+
Coord C1 exon
chr20:5553863-5554064
Coord A exon
chr20:5554065-5554272
Coord C2 exon
chr20:5554273-5554451
Length
208 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
TGACAGCTTTGTCCTTCCAGGAA
3' ss Score
8.96
Exon sequences
Seq C1 exon
GTTTACCTCAAAGGAGGACTTCCTGGGCTTCATGAACGAGTTTCTGGAGCTGGAGTGGGGTTCTATGCAGCAATTCTTGTATGAGATATCCAACCTGGACACACTGACCAACAGCAGCAGTTTTGAGGGCTACATAGACTTGGGCCGCGAGCTCTCCACACTTCACGCCCTGCTCTGGGAGGTGCTGCCCCAGCTCAGCAAG
Seq A exon
GTCAGTAGATGTCCCCTCTGTCCCATCCCCAGGAACTTCCACAGGCACCCAGGCTGAGAGACTATCTCTGCACACAACTCTCACCACCTTCCCGTTCCCAGAAACTCACCACCACTTCCAACACACCTCACGACACCTCTACCCGTGGCCTCCGAGGCCCTTTTAGGACTGGGCACTCACTCACCAAGTGACAGCTTTGTCCTTCCAG
Seq C2 exon
GAAGCCCTCCTGAAGCTGGGCCCGCTGCCCCGGCTCCTCAGCGACATCAGCACAGCCCTGAGGAACCCTAACATCCAAAGGCAGCCGAGCCGCCAGAGCGAGCGCGCTCGGTCTCAGCCCATGGTGCTGCGCGGGCCGTCAGCCGAGATGCAGGGCTACATGATGCGGGACCTCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000483:ENSRNOT00000000572:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.567
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF120043=DUF3498=PU(8.1=78.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCAACCTGGACACACTGACC
R:
CTGTTGAGGTCCCGCATCATG
Band lengths:
293-501
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]