RnoINT0146734 @ rn6
Intron Retention
Gene
ENSRNOG00000000483 | Syngap1
Description
synaptic Ras GTPase activating protein 1 [Source:RGD Symbol;Acc:621090]
Coordinates
chr20:5555457-5557176:+
Coord C1 exon
chr20:5555457-5556528
Coord A exon
chr20:5556529-5557002
Coord C2 exon
chr20:5557003-5557176
Length
474 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
CCCCTCCTTGCTGGTCACAGCAT
3' ss Score
6
Exon sequences
Seq C1 exon
CTCTATGGACATGGCTCGCCTCCCCTCCCCAACCAAGGAGAAACCCCCGCCGCCCCCTCCCGGTGGGGGTAAAGACCTGTTCTATGTGAGCCGGCCACCACTGGCCCGGTCCTCCCCAGCATACTGCACGAGCAGCTCGGACATCACAGAGCCGGAGCAGAAGATGCTGAGTGTCAACAAGAGTGTGTCCATGCTGGACCTGCAGGGCGACGGGCCTGGGGGCCGCCTTAACAGCAGTAGTGTTTCCAACCTGGCAGCTGTTGGGGACCTGTTGCACTCAAGCCAGGCTTCACTGACAGCAGCCTTGGGGTTGCGGCCTGCACCTGCCGGGCGCCTCTCCCAAGGGAGTGGCTCTTCCATCACAGCAGCCGGCATGCGCCTCAGCCAGATGGGTGTCACTACGGATGGTGTCCCCGCCCAGCAACTGCGCATCCCTCTTTCCTTCCAGAACCCTCTCTTCCATATGGCTGCCGATGGACCAGGGCCCCCAGCAGGCCATGGAGGGAGCAGTGGCCATGGTCCACCTTCCTCCCATCACCACCACCACCACCATCACCATCACCGAGGGGGAGAACCCCCAGGGGACACTTTTGCCCCGTTCCATGGCTATAGCAAGAGCGAGGACCTCTCTACAGGGGTCCCTAAGCCCCCTGCGGCCTCCATCCTTCACAGCCACAGCTACAGTGATGAGTTTGGACCCTCTGGTACTGATTTTACCCGTCGGCAGCTCTCACTTCAGGACAACCTACAGCACATGCTCTCCCCGCCCCAGATCACCATCGGTCCCCAGAGGCCAGCTCCCTCAGGGCCAGGAGGGGGCAGTGGTGGGGGCAGTGGTGGGGGCGGTGGGGGCCAGCCACCTCCCTTGCAGAGGGGCAAATCTCAGCAGTTGACAGTGAGTGCTGCCCAGAAACCCCGGCCGTCCAGCGGGAACCTATTGCAGTCCCCGGAACCAAGTTATGGTCCTGCCCGTCCACGGCAACAGAGCCTCAGCAAAGAGGGCAGCATTGGGGGCAGCGGGGGCAGCGGTGGCGGAGGGGGTGGGGGGCTCAAGCCCTCCATCACCAAGCAG
Seq A exon
GTAGGTGAGGGTAGGGTAAGGTGGCGTGGGTGAAGAGCAGGGAGGGAAGCAATAGTATAGTCTGGTGTGACAACTTTCTCACCTTCTTTGTTCACTAAACAAACGTGTGGCATTTGGCTTGTATTCTCACCGTTCAGGAGGCAAGGTGATACAAGGTGACACGAGTTCTGAGGGCAGCTAGGGCTAGGTAGTGGTATTGTCTCTAAACAAGAAGCTGACAAACGTAAGGAGAGAGCCCTGAGCAATGTCCTGTGAACCGAGGCACCGAGGGTGTGTGGATGAGCAGTGGAGGAGCCCAGCCTTGCCCCTCCTCTGGGCAGGCCGGCAGGCAGGCAGGCAGGATTGCCTCACTAGTGCAGAGGGAGCAAGGCTCAGGCAGGGTGCAGGCCTGGGGGTCATTTCTGTGTTCTCTGCCTCTGAGCACGCCCTCCCTTTCCCACCTTTCTGCTCTCTGCCCCTCCTTGCTGGTCACAG
Seq C2 exon
CATTCCCAGACTCCATCCACGCTGAACCCCACGATGCCGGCCTCGGAGCGGACTGTAGCCTGGGTGTCCAATATGCCTCACCTGTCCGCTGACATCGAGAGTGCACACATTGAGCGGGAAGAGTACAAGCTGAAGGAGTACTCGAAGTCCATGGACGAGAGCCGACTGGACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000483:ENSRNOT00000000572:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.950 A=NA C2=0.948
Domain overlap (PFAM):
C1:
PF120043=DUF3498=FE(61.6=100)
A:
NA
C2:
PF120043=DUF3498=FE(9.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGCAGTTGACAGTGAGTGC
R:
TCTCGTCCATGGACTTCGAGT
Band lengths:
350-824
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]