RnoINT0146742 @ rn6
Intron Retention
Gene
ENSRNOG00000000483 | Syngap1
Description
synaptic Ras GTPase activating protein 1 [Source:RGD Symbol;Acc:621090]
Coordinates
chr20:5547037-5548783:+
Coord C1 exon
chr20:5547037-5547158
Coord A exon
chr20:5547159-5548629
Coord C2 exon
chr20:5548630-5548783
Length
1471 bp
Sequences
Splice sites
5' ss Seq
CCGGTAGGT
5' ss Score
9.39
3' ss Seq
TCTGAACCTTGTGCTGCCAGGGC
3' ss Score
5.56
Exon sequences
Seq C1 exon
CAAGGCTTCCTGAGCCGGAGGCTAAAAAGCTCCATCAAACGTACAAAGTCACAACCCAAACTTGACCGGACCAGCAGCTTTCGACAGATCCTGCCTCGCTTCCGAAGTGCTGACCATGACCG
Seq A exon
GTAGGTACAGGACCTGAAATGAGGTGGGTGGAGTGGGGGTTCCCTGAGGATAAAGGTCAACGGGCTCATGCTGGTTGGGGTGCAAGAGACTTCAGGGAGGAGCTGGCCTAAGCTGTGGGTGGCAGGAAAGAGGGACAGACGACCTGCCCAGGCAGGGGAGGAGGTGAAGGTGAAGCCAAGGAGGTCAGGAGGGCTCGCAGAGTGGACGAGCTAGGCCTCAGAGACCCCAGCAGCAGGGCCAGTGGGGAGCCACAGGACAATGGGAAAGGAGCCTCTGGTATGCAGGTAGCAGAATGGGGCAAAGGCTGGAGCTAATCCGGGCCTGAGGAAGCCTGCTTGCCTTCTGCCCTTCCCTGGGCTTCCCCTCGTCCAGTCGCTCCTGGAGAGAATCTGTCCTTTTCTCTGCATCTGCTCTCCCAGGGACTGAGCAGGGTAGGGAGGTTGGGACACCTTTCCCTGCCCCCTTCCAAGTAACCAGTGCTGGATTTGGGGCTGGAGGGGGGGGTGAGGGCATGGTATTCCTGGCCGCGGGGGCGGGGGGCCGGGGGAGCGTGGTGCTGACGGCAGCCAGAGCCTGTGATGACGGGGCTGCTATAAATAACTTCACGGAGGCTCCCACACCCGAGCTCCCCTCCTGCTTCCCCATGCTCTCCATCTTGGTCCCCTACCCATTTCCACACCACTTGGTGTCCTTGCTCCCCTCGCTCTGGTACCTCATCCCAGTTTATCCCCTGCTCCCGGTGGCACAGCACTGTGTGCGCGTGGCCACCCTGGTCCGTGCTCCGTAAGGAAGAGCTTGCTCTTCCTTAGCCTTCCTGCGCCTGCTTTTGCCTCCCCCTGCTGTGCTGCCTCCTCCTCCCCATGTCTGCTCCCCAGCCTCTGACCTCTATTCTGCCCCCTTGCTCTCTCCTGTCTTTCTCTCTTTACCCCTGGTTGTATTAGAAACTCACTTCATTTATAGTTTGAATCATAAAATGTTTATTAGATACTAACTGTGTGCCAGGGCCAAACCAGACATTACTGTATTTCCTCTGTGACTCAAGTCTTTGCTTCCAGTTTTTCCTTTATATTGAGATTCTGGATTCTGGAGTCACCTAAACATGTCCAGGCCATTTTGTTTTTTCCTTTTCTTTTTTGCTGCTGCTTTTTTGTTTTTGACATGGTTTGTTTTGGGTTTTAAAGACAAGGTTTCATCATGTGGCCCTGGCTAACCTGGGACCTGCTATGTAGACCAGTCTGGCCTCAGACTTAATAGGGATCTACCTGTCTCTGCCTCCTGAGTGCTGGGATTAAAGGTCTGTGTTACTCTGCCCAGGAATTCTGAGTATGAGTTGACTCAGATAAGTCCCTTGAAAGGCATTGGTTTCCCCTAACCTGGGCTTCCCCTGTGAGGCTGTGTGTGATGGACTGAGGCTCTCCTCTGGCGAGGAGAGGGCCTTCCCTGATTCTTCTCTGAACCTTGTGCTGCCAG
Seq C2 exon
GGCCCGGCTGATGCAGAGCTTCAAGGAGTCTCACTCCCATGAGTCCCTGCTGAGTCCCAGCAGTGCTGCTGAGGCCCTGGAGCTCAACCTGGATGAAGACTCCATTATCAAGCCAGTACACAGCTCCATCCTGGGCCAGGAGTTCTGCTTTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000483:ENSRNOT00000000572:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.341 A=NA C2=0.231
Domain overlap (PFAM):
C1:
PF0016924=PH=FE(18.1=100)
A:
NA
C2:
PF0016924=PH=FE(23.1=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:
CCGGAGGCTAAAAAGCTCCAT
R:
CTCAAAGCAGAACTCCTGGCC
Band lengths:
262-1733
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]