RnoINT0146728 @ rn6
Intron Retention
Gene
ENSRNOG00000000483 | Syngap1
Description
synaptic Ras GTPase activating protein 1 [Source:RGD Symbol;Acc:621090]
Coordinates
chr20:5535547-5538905:+
Coord C1 exon
chr20:5535547-5535568
Coord A exon
chr20:5535569-5538783
Coord C2 exon
chr20:5538784-5538905
Length
3215 bp
Sequences
Splice sites
5' ss Seq
GAGGTACGG
5' ss Score
9.4
3' ss Seq
TGTGTGTCTCTGTCCCCCAGATG
3' ss Score
12.37
Exon sequences
Seq C1 exon
ATGTCCTATGCCCCCTTCAGAG
Seq A exon
GTACGGTGGTGGTAAGGGTAGGGGAGGGCCATATGGGGGGGCAAGAGGGGGAGGGGCAGGGGGCGGGGGAGGGCCAGGGCCACCGAGGGGAAGGAGCGGCTGAAATGGAGGGAGAGGGGAGGGCTGGAAAGGCAGAGGTGGGAACAGTGGGAAAGGAGGGATTAGAGGCATAGGGGTAGGTAAGGGATAGAGGGGCTGAGATATGGGCCCTGAAAGGGGCTGAGGGGAAGTGATGGAGGGAAAGCGCGTCAGAAAGGGATGAGAAGGGAGGACTGAGTTTGGGGAAAGGCTGCAGAAATGGTTTGGATTTGGGAGCTGAGTGAGGAAGAAATTACCAAGGAAATAGAGGCACGGGCTTAGGAGATGGGTAGAGGGGAAAATGAAAACACGGGCGGCGTGAGAGACCAAGGAGATGGGAAGGGAATTTGGTGAGGGGCTCGGGGTGATAGGACTTAGGAAAAGAGTAGAGGAGGGAGGGAGGGAAGGGGGCCAGATGGAGAAAGAGGGTGGCAGTGGGGGGGTGGGGGGTCCAGATGGAGGGAAGAGAGGAGAGAGAGAGAGGGTTGGGGGAGGGGACGCCAGAGAAGGGGGAGGATCAAGTGTTTTTTTTTTGTTTTGTTTTTTTTTTTGGTTGGGTTGGGGGGAGATGCATTTAAGATTGAGGGATGGTTGCAAGGGCCAGGTAACAATTCTGAGGGCGACTGGCTCTTAGAAGTGAGATGCAGTCTCAGGGTCTCATTTGCTTCCTTCACTTAATCGCTTTGACCCCTTCCCCCACCCCACCTCTTCTTTCCAGTCCCCCTCCCTGCCTCTGCTGTCCATCAGTTATATCTTTCCCCCCATATGGTGTCCGTTTCTTATATGAGTCCCCCTTCTGTCCTTCCCCTGTATTGGTCCCTACCTCATATCTCTTCTCTCTCCCTCCCCTTTTCTAATAACTACCTTAGTACATCACTGCTGCTCCCGGGCTCTGTGTGTGTCTCAGCCCCCGTCGGGCCCTGCTCACCCATGTTGGCTGAAACCTTCTGGTCCATTCACTTGCCTTAGGCATACACCACCATCATTACTTCCTTTTCTCTTAGATCCACCCTGTTACTTGTCCCTCAGCTCACCCTCTGTTTCCTATCCCACTTCCCATCTTGTCACATGGTTATTTCCTCTTATGCCCCAACCTGGTGATTCCTCTCTTCTTGTCCCCTCTGCTTCCTTGGGTGATGGAGATTTGGGGGGGTACCAAAACATGGGTTTTGATGGTTGGAACAGGGCTCTAGGGAATCCCCGTCTTGGACTCTTGTGGAATTTGTCATTCCAGTAAAAATTTCCCATTTCCCCTTTCTCTGCCATGTTCCATCATCTCCCAGGGTCACTAGTGTACTTAACTATAGACTGTGTGTGTGCCTGTGTGTGTGTGTGTGCTTGCATGTATGTGTGTGTATGTGTGCATGTGTGCCTGTGTACGCGTGCATGTGTGTGCGCATGTGTATGCATGTATGCATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGCGTGTGTGTGTGCGCATGTGTAGAGTTGAACCTAAGCTAAGGTCCCCTGTGTCCCTTTCCTGTTCCCAGTAGAATAGTGTCCCTTGAGGTCTAACCTGCTTGCCCCAGCTGTAGCCTGGAGCAGCTGTTGTGTCTTGCTTACATGCATCCACAGATTTTCCCTCTGGGTCCACCATGTGTTGAGATGAACTAGGCCTCCAATGGCTGCGCTCTAAGTTATGGGTGGAGGGTGTTGCTGCTGTTGTGCTGGGGCTTTGAATCCTAGTGGGATTTTTGTTGTTGCTGTTGTCGGTTTTGGGGGTTGTTGTTGTTATTGTTTGTTTTGTTGGGTTTTTTTTTCCCTACCACTGAGCTATAATCCTCAGCCCCACCAGTGATCTTTGATATTTAGAGAATACGAGGAGAGTCTCCAAGAAAGCATCAAGACAGTGAAATTCTGAAAGCACTGTGAGGTTTAGGCACAATTCCCCAGGTGTTCATCTTTCTGTCTGACCTGCGATTTGGGTAAATATGACCATCATCGGTAAGGGGATGGAGTTCCCTAAAGTTACTCAAGGGACTGGAACGAAGCTCAAAGGCCAGTTCTCCTGAAAGGTGCCCAAGTTAATTACCCCACAAAGGTGACAGCACTGGGATTTTCTTCCTGTGAACATTCTCCAACTGATCTCTTAAGCCTAGACTTATCACTCCAATGTCACCAATCTAACTTTTCTGACTCCCTTAAGTCCTTTCCTTCACTATGTCCCCAAAAATGGTCTATGGCAACAATGCTAGCAAGACAGCCAAGATGTCTCAGGGAGATCCTCGGACAACTGTTGGTCCTTCCCCGCTCCCCCCACCCCCAAATCTATCTTCAGATCCTTGGGAAGTTCCTCTGTCATCAGGCCTGGCTGTTCCGCTCTCCTCCACTCTTTCTTAAGTTCCTCACTGTGCCCAATGACAGCCAGGTGCGGCTGTCAACCTGTAGAGTTGGCTTCATTTCTACCTATGAAGCTTAGGTGGGGAGAGGAGGATTGACTCTTGACTCCTGAGCATGTTGTGAACAGAAAGGCCAATCCCATCTCTGGTCATCCAAGCAGTATACTCACAACCTTCTCCCACCCTGATCCCCCTGATAACATCAGGATAGAAGTGGGTAATTAGGAAGGGAAGAAGAGAGGGGAGGCCTCGTGCCTCTCTGAACATGTAAGCCCCCCTTCCTCTCTTCTAAATGTTTATTTCTCAGGATCTCATGTCTCAGATATTCTTCAGAATACCGTCTTCCTCTCTACAGCTGGGCACCTCAGATTCTCCTAAACGTGTGAGGCCACATCCATTGTGAACAGCTTGTCAGTTCCTCTCCTCTGACCTCTCTGTCTTTTGCCAGTTTCATAAACCTCTCCAACACCCCTCCAACATTGGGGCAGAGTTTTCCCATTCTCCTGCCACCAGTAAAGTCCCTCTGTGTCATAAGACTAATTCTCATCTTTGAAACCAAGCCCATCCCCTCCCTGGAGCCTCCTATGATGATGCCACTCAGTGTGAAAGACCATCTTCCGACCCTTTAAAACCACCAGGCATTTCACACCGAAGACCTCTCTGGGCAATCCCTCCTCCCTCTTTGCAGACTCTCCTCCCCGCTCTAGGTTTCTACACCCAAAGTATAGACCCTCCCTCACTGCTTGTGTGTCTCTGTCCCCCAG
Seq C2 exon
ATGTACGGGGACCCCCTATGCACCGAACCCAATACGTTCATTCCCCGTATGACCGTCCCGGTTGGAACCCCCGGTTCTGCATCATCTCTGGGAACCAGCTGCTCATGCTGGATGAGGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000483:ENSRNOT00000000572:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.489 A=NA C2=0.305
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0016924=PH=PU(14.5=78.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]