RnoINT0146736 @ rn6
Intron Retention
Gene
ENSRNOG00000000483 | Syngap1
Description
synaptic Ras GTPase activating protein 1 [Source:RGD Symbol;Acc:621090]
Coordinates
chr20:5558424-5560242:+
Coord C1 exon
chr20:5558424-5558635
Coord A exon
chr20:5558636-5560151
Coord C2 exon
chr20:5560152-5560242
Length
1516 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
ACTGAAGCCCGTCCCTTCAGGCT
3' ss Score
4.16
Exon sequences
Seq C1 exon
GTGAAGGAGTACGAGGAGGAGATCCACTCACTGAAGGAAAGGCTACACATGTCCAACCGGAAGCTGGAAGAGTACGAGCGGAGGCTGCTGTCCCAGGAAGAGCAGACCAGCAAGATCCTGATGCAGTACCAAGCCCGCCTGGAGCAGAGCGAGAAGCGCTTGAGGCAGCAGCAGGTGGAGAAGGACTCCCAGATCAAGAGCATCATTGGCAG
Seq A exon
GTGAGGGGCGGCCCGGGGAGGGCGAGGGCGAAGGGGAGACCTGCTCAAGGTGTTGAGCGGTCGATCCCTTACCGCCAGCACTGCTTACACACAACTCCCGAGGCCCCAGGGAGCTACAGCAGTGCCTTAGTCTAGCCATCAGCATCCCTCCCAGCTCTCCCTAATCCACAGCTCCCCCAGCAGTGCCTACCCACTCCTGTGTCCCTGGCCGGAGCTCCTTGTTCAGGCTTGCAATGGGTTCCATTAGATGAGGTTTTAGCTTGTCAGTGCCCCAAAGGACCTGCTTGCTCCTCAGGGGCCACCACAGCCAGAGCCAGGTGTGCTCTGATCTAGTGTCATGTGAGACATTTGATACCACTGCAGGGACTGTCTTATGAGACCGCTTCAAAGTCTTCAGTGACTCAGGCACGGGGCACTGAAGCTCCGCCCTCTACGCAGGCGCAGGGCTTCTAGGCTCTGGCTGGCAGCATCTTAGAGATACAGAAGCCTAGCTGTACGCAGTTGTGCACACTTTTTTGGTTGTTTTGAGAGAGGGTTTCTCTGTGTAGCCCCGGCTGTCCTAAAACTCGCTCTGTAGACCAGGCTGTCCTCAAACTCAAGAGATCCACCTGCCTCTGCCTCCCAAAAGCTGGAATTAAAGGTGTGCACCCACACCACCTGTTTACTTGTGCACACTTTGAATGTGTCTGTAACCCCACATTTAGGAGGCTGAGGCAGGAGGGTGATCTCAGCTCCACGGTGCGCTCTAGGCTTCCCTGGCTACAATGTGAGACTCCATCTGAAAACAACCAATGGGAGAGATCAAGTCTGCTTTCATGGGTTTGAGAGATGACTCAAGTGCTTGAGAGGACACACAGCTTTTCTAGAGAATCTGAGTTAAACTCCCAGCACCCACGTCGGGTGGCTTCTCACTCTCTGTAACTCCAGTGCTACAGGGGCGTCTGATACCTTGGGCCTCGGTGGGCTCCTGCACTTGTGTGGGCTCCACACACAGATACACAATTAAAATATATAACAGGCTTGGTGGCAGTGGGGTGCACGCCTTTAATCCCAGCACTCAGGCGGCAGAGGCAGGCAGATCTCTGAGTCTAGTAGAGTAAGTTCCAGGACAGCCAGGGCTACACAAAGAAACACTGTCTCAAAAACAAAGAAATAAGAAGCTGGGTGTGCGGATCCTTGCCTTTAATTCTGTCACATGGGAGGCTAGGGCAGGCAGCTCTCAGAGACAAGGTCAGCCTTGTCTACACAGTGAGGTCCGGGCCAGCCAGAGCTACACAGTGAAACAACATATGTGTCTCTAAAAAGCCCCAGGAGGCAGGCATGAAGATCCCTGGGAGAAAGTGGAAAGCAGACTCTGGTGACAGCGTCTTTTGGGTACTGGGGGAGGAGGAATTCTGCGAGGAGGGGAATGTCCAAGGTTTTTCCAGAGTTGCAGGGGTTCCCCAAGGCCAAGAGTACTACAGGTGGGCTCTGAGTCCGTGCCGGCCACTAACCCCACTGAAGCCCGTCCCTTCAG
Seq C2 exon
GCTGATGCTGGTGGAGGAGGAGCTGCGCCGGGACCACCCCGCCATGGCTGAGCCGCTGCCTGAACCCAAGAAGAGGCTGCTCGACGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000483:ENSRNOT00000000572:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.568 A=NA C2=0.505
Domain overlap (PFAM):
C1:
PF120043=DUF3498=FE(12.1=100)
A:
NA
C2:
PF120043=DUF3498=FE(5.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGAAGGAGTACGAGGAGGAGA
R:
GAGCAGCCTCTTCTTGGGTTC
Band lengths:
294-1810
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]