RnoINT0146744 @ rn6
Intron Retention
Gene
ENSRNOG00000000483 | Syngap1
Description
synaptic Ras GTPase activating protein 1 [Source:RGD Symbol;Acc:621090]
Coordinates
chr20:5548986-5551547:+
Coord C1 exon
chr20:5548986-5549084
Coord A exon
chr20:5549085-5550923
Coord C2 exon
chr20:5550924-5551547
Length
1839 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTG
5' ss Score
7.76
3' ss Seq
CAACCACGTCCTCATGCCAGGAC
3' ss Score
6.32
Exon sequences
Seq C1 exon
GTAACAACATCGTCTGGGACAAAATGTTTTGCCTGTCGGTCTGCAGCCGAAAGGGACAAATGGATTGAGAATCTACAGAGGGCTGTGAAACCCAACAAG
Seq A exon
GTATTGAGGAGAACGGGAAACAAGGGGCAGGGCCTGTGGGCTAAGGGAGGGGGTTTGGGAGGAGAGGGCAGGTACCAGGGCCCAGGTGATTCCCATTATTCAGAACCCCCGTTTATTTCCCTTTCTCCCCATCTGCTACCTTATATCACACCCTGCTTCGCTGACATGAGAGTCATAGTGCTAGGGGGCCAGCCAGCAGGACCTGTTGGGCCCTCCAGTTCAGTCTAAGGGCCAGCCGGAAGGCCTCACTTGCCTAACAGGTTGTTATCCAGCCCCACTCACAGTGCTCTGTGAACCCTGGCTCTTTTTACAAAGTCTTCACAAGCATGGTTGGACTCTGTGACCTCCAGGTCCCCTTGACAGGGCCCCTGTGCATCTGTGTTTCAACCAAGACCTATGTTCCACCAGGATAAGGTGCCACTCTGTCAGCTGGTCTCTGACTCCAGTTTGTGGCAGGCTCACAGTCCTGGCCATCTTTCTCTTTCCCCCGAGGGCCTTTATTAGGAAGTCCCACTTAAGTGCTAGACACAGTCGAAGGCACACAGGGTCTGCACCGCACTCTTTCAGCACTGTACTACTGGCCTGCGACTCCTACCAGCAGCTTAAGCTGGCCCTCAGGCACTGCACTGGCTCCACATGTAACACAAGCAGTATTTTGTTTTTGCACATCTGACGTTTCTGTGGGATTTTCTCATCTGAATCTTTAGGGTGTTCCTTACTTTAAAAAAAATGTTGCTGGGCGTGGTGGCACAGGCCTTTAATCCCAACACAGAAGTGGGTGGATTTCTGTGAGTTCAAGGCCAGAGTGCATTCCAGGATTGAGCTTTGTGGAGTAAGAAAACCAAAAGGAAATAACATAAAAACTTCCTTATTTATTCAGTGGGGATGGGGTGGGGGAGGGGAGGTCACAGTGCACAGATCAGAGCATGGCTTTCTGGACCTGGTTCTTTCCTTCCACTCTGTTGTGGGTCCTGGAGCGTACACCCATGCTTGGCACCTTCCCCAAGTAAGTCATCTTGTTGGCCCTTCCCTGCTTTTGACCTGTTACTCAAGCATTTTCCAGCGTGAATTCTGTATGAGCTGCCCTTCTCTGTTAGCTGCCATGGCTGCTGTAAAAAGCCACCATGAACTGAACCAGCTGAAGCCATTCCCTCACTGCTCAGGGGTCTAAGTCCAGCGTGAGCAAGGCCGTGTCAGTTCTGAGGCCGTTACATTCAGTCCTTCCCTCTTTATGCAGCTGCCTTCTGTCTGTATGTCTCTAAATGACCCTCTCCATGTGATAAAGTCACCAATAGATGGATTAAGAGATTATATATATTTTTTTTTAAGATTTATTTATTTATTATATATAAGTACACTGTAGCTGTCTTCAGACACACCAGAAGAGGGCATCAGATCTCTTTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCATGACCTCTGGAAGAGCAGTCGGGTGCTCTTAACCGCTGAGCCATCTCTCCAGCCCAAGAGATTATATTAACATCTGTCAGGTCGCTCTTTCCGAATGACATCACACTCAGATTCTAGAGAGGCGATAATTTGAGGTCATGGTTAGATAGAGTGGTGCATGTACTTCTGGTACTCTCGGGTACATATGCTCATTTGAGGCCAGCCTGGGCTACTTAGTGAGCTATCTCAGAAACCAAAACCAGGTACAGTAGAATTTTGGGAGTGGTGGACGCTATTAAAGCCCAGTATACTTACTGCTAACCCTATGGCCACCATCTTGAGCCCACGTGCTCACTGTCCTGGTGTGTCTGTCTTTACCCATTTATCTGCCCCAACCACGTCCTCATGCCAG
Seq C2 exon
GACAACAGCCGCCGGGTAGATAACGTGCTGAAACTATGGATCATAGAAGCTCGAGAGCTGCCCCCCAAGAAGCGATATTACTGCGAGTTATGCCTGGACGACATGCTCTATGCACGGACCACTTCCAAGCCCCGCTCAGCCTCAGGAGACACTGTCTTTTGGGGCGAGCACTTCGAGTTTAACAACCTGCCTGCTGTCCGGGCGCTGCGGCTGCATCTGTACCGTGACTCGGACAAAAAGCGGAAGAAGGACAAGGCAGGCTACGTTGGCCTGGTGACTGTTCCAGTGGCCACCCTGGCTGGGCGCCACTTCACAGAGCAGTGGTACCCCGTGACCCTGCCAACAGGAAGTGGGGGCTCTGGGGGTATGGGCTCGGGGGGAGGAGGGGGGTCAGGGGGCGGCTCAGGGGGCAAAGGGAAAGGAGGCTGTCCTGCTGTGCGGCTGAAGGCCCGTTACCAGACAATGAGTATCCTGCCCATGGAGCTATATAAGGAGTTTGCAGAATATGTGACCAACCACTACCGCATGCTGTGTGCCGTGCTGGAGCCCGCCCTCAATGTCAAGGGCAAGGAGGAGGTCGCTAGTGCACTGGTTCACATCCTGCAAAGCACAGGCAAGGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000483:ENSRNOT00000000572:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.121 A=NA C2=0.115
Domain overlap (PFAM):
C1:
PF0016924=PH=PD(13.1=87.9)
A:
NA
C2:
PF0016825=C2=WD(100=38.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGGCTGTGAAACCCAACAA
R:
GTACCACTGCTCTGTGAAGTGG
Band lengths:
349-2188
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]