RnoINT0146729 @ rn6
Intron Retention
Gene
ENSRNOG00000000483 | Syngap1
Description
synaptic Ras GTPase activating protein 1 [Source:RGD Symbol;Acc:621090]
Coordinates
chr20:5551998-5553777:+
Coord C1 exon
chr20:5551998-5552142
Coord A exon
chr20:5552143-5553540
Coord C2 exon
chr20:5553541-5553777
Length
1398 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGA
5' ss Score
6.29
3' ss Seq
TCCCCACCCCTTCCCCTCAGCGT
3' ss Score
9.37
Exon sequences
Seq C1 exon
GGGAGTTCATCCGGGCTCTGTATGAATCTGAGGAGAACTGTGAAGTAGACCCCATCAAGTGCACAGCGTCCAGTCTGGCAGAGCACCAGGCCAACCTGCGGATGTGCTGTGAGTTGGCCCTGTGCAAGGTGGTCAACTCCCATTG
Seq A exon
GTGAGACTGGGGACGCTGGGCTGGGGGGCCAGGGCTGGGCGGTTGTGTGTCCATCTGTTCATCCGTCTGTCCATCTTCAGAGAACTGAGCATCAGTACGGGCAAAGCACTTTCTGGGGTGTCGTAGAACAGAGAGAGGTGGACAGGGCTGGCTCCTGACCTCAGATGGCCTCTGACCAAAGTGATCAGGGATGCACGAGATGCTCGAAAAGCCACAGAGCCATTGTGATGTGTCCCATTGAGGGAGGGTCCCTCGGGCAGCACCAAGTCAGAGAAGATGAAGGCGTGTGGGGTGCCCAGGGCTGGGCTGTGAGGATCGGCTCGGGCTAGTATTTGTACACAGTAGGCAGAGGGCGTTTCCGGGGCAGTAAGATAGCACAGGTGAGGGAGGTGGTGTGAGAAGGCTGTGATCCTTCAGAGGTTGGCTGGCAGCTGCAGCCATGGCTCTAGTGGAGGCAATAGCGGGGAGAGAGCTGTGCTTTGGGAAGGAGAGAATCTGGAAGTCCAGGGTTCAGGAGTCTGCAGCCATCAGAACACTTTGGGGTAGGCTTAAAGGTGTTGGCATCAAGAAGCATGGCTGAGACTGGCCCAGAAGTCAGTGAGCTCCACGGTGAAGGAAAGGGGGAAGCACAGTCCCCGTGAGGCTCTGGTTCCGGTGTGAAAACCAGATGTAGATCCAGGTAGAGTTAGAAAGTCTAAAAGGGGCTGCTCAGGTCGGCTAGCGGAAGGACAGGGATTGTCTGAGGGGTTGTGCGTGCGCAGTCAGGATGACTCCAGGTCATGAGACTGTAGTGCTTAGGGACCCACAGCCTCATTGGCAGAACCAGGGGAGTCTAAAGGAGGAGCCAGCTGGCAGTGTGGGGGCGATGGTGAGCTGTTTTACAGTGTCAAGTTTAAGGTGTCAGTGGGACATTGAGGTGGCGCCGGGAAGGAGGCGGGGAAGAGTGAGCCGAGCCATCCCAGGGCTGGGATCATGCCTGGGCACGCCCATCCCCATTTCCCTGGAGTCCAGAGAGTTGGGGGGTCCGAGCTCCCTGTGCCTCAAGTGACCCTCCATCTCTCTCCCATCTCTGTCTCTTCCCTCGTGTCTGTTTTTCTTCTCCTCCTCTCCTTGTCTCTCTCACGCCCTCTTTGTCTCTCTCCCCGTGTCTCTCTCCCCTCACCCCTTCCCCCTCCATTTCTCTCTCCGGAATCTGTTCCCTTTCCCGTGGCCCTCTTCTTCAGCAGCCTCCTGTCTTTCTCCTGCAGTCCCTCCCTCCTGGTCTCTCACCTGTCTCCACACCTCCTCTCACCTCCTACCACCCCTCAGCATGTTCCCTGAAGGCTGAGGGTCTCTGGGGCTCAGTCCCGGTCTCTCTTTCTCTCTCTCTCTCTCTGTCTCCCCACCCCTTCCCCTCAG
Seq C2 exon
CGTGTTCCCGGGGGAGCTGAAGGAGGTGTTTGCATCATGGCGGCTGCGCTGTGCAGAGCGGGGCCGGGAGGACATTGCTGACAGGCTGATCAGCGCCTCGCTCTTCCTGCGCTTCCTCTGCCCGGCCATCATGTCGCCCAGTCTGTTTGGACTGATGCAGGAGTACCCAGATGAGCAGACCTCACGAACCCTCACCCTCATCGCCAAGGTTATCCAGAACCTGGCCAACTTTTCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000483:ENSRNOT00000000572:10
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=0.000
Domain overlap (PFAM):
C1:
PF0061614=RasGAP=FE(27.9=100)
A:
NA
C2:
PF0061614=RasGAP=PD(44.2=95.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGTTCATCCGGGCTCTGTA
R:
TAACCTTGGCGATGAGGGTGA
Band lengths:
356-1754
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]