HsaINT0162802 @ hg19
Intron Retention
Gene
ENSG00000227460 | SYNGAP1
Description
synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:11497]
Coordinates
chr6:33406552-33408742:+
Coord C1 exon
chr6:33406552-33406696
Coord A exon
chr6:33406697-33408505
Coord C2 exon
chr6:33408506-33408742
Length
1809 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
TCCCCGACCCTTCCCCCCAGCGT
3' ss Score
8.98
Exon sequences
Seq C1 exon
GAGAATTCATCCGTGCTCTGTATGAATCTGAGGAAAACTGCGAGGTAGACCCTATCAAGTGCACAGCATCCAGTTTGGCAGAGCACCAGGCCAACCTGCGAATGTGCTGTGAGTTGGCCCTGTGCAAGGTGGTCAACTCCCACTG
Seq A exon
GTGAGACTGGGAACGCTGGGCTGGGGGGCCAGGGTCGGGGGAATTATGTGTTCATCTGTTCATCTATCTGTCCATCCTCAAAGAGGACTGAGCACCATTTATGGGCAAAGCATTGTTCTAGGCGCTATAGAGCAAACAGGTGAAAGAGGCCTGGTCCCTGCCCTCAGAGGGCCTCCACCAGAATGGGGACAAATTAGAAGAAAAAAAAAAAAAGCCACAGAGCCATAATGGTGTGTAAGTGCTGAGTAAGGGTCCCCCCAACCTCTGTGTGACATAAGGTCAGAGAGAAGGCAGAGCTTTGAGATAAGTGGGGAAGAGGTGCCCCCTTGGGTAGGCTTTGAAGACTGGTTTAGGTTCTGATATATGGACATAGTTGGCAAGAAAGACATTTCAGAAGAAGGCTGTGAGAAAGGCACATGTGTGATGGTGAAAAGGCCCAGGAGTTTTCAGGGGACATTAAAGTAGGTTAGTAGCAATTACATCAGGTTTAGTGGAGCATGTGCCTCATAATGGGGAGTGGCGGGAGAGATGTCTGGGCAGGAAGATTAGCTTTAGAAACTGGAAGGCCTCAAGGAGTCTGAGGTCATTGGTAGGCCTTGGGATGCCATTAAAGGTGTCAGAAATATTGTGATTTAGAAGATTAATCCATAGGCTGGGCACGGTGGCTCACACCTGTAATACCAGCACTTTGGGAGGCTGAGGCGGGCAGACCACCTGAGGTCAGGAGTTTGAGACCAGGCTGACCAACATGGAGAAACCCTGTCTCTACTAAAAATACAAAATTAGCCAGATGTGGTGGCACATGCCTGTAATCCCAGCTATTCGGGAGGCTAAGGCAGGAGAATCACTTGAATCTGGGAGGTGGAGGTTGTAGTGAGCCGAGATCACACGATTGCACTCTAGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAATTAATCCATAAGTAGAGTGTATGTAGTAGAGTAGAGGGATGTATGTTGGGGGATGACTGGAATAGAGCCAGCTGGGGGCTCGGAGGCATGAAAGTCAGATCCTGAATCAGAACAGTGACAGAAGTTAGGAAGGAGCTACTGGAAGGACCCTCTCGGGAAAGGATCAGTAGGAATTGTCAGCTTATTGGAAAGGAGGGAGCATGTCTGTGGGGAGTCACGGATGACTCAAGAGGCCATGAGGCTGGTGGTTGGGAGACCGGTGGCCTCATTGACAACCAGGAAAGTCAGGAGGAGGAGCCAGTTGGAGGTGTGGGGGCGATGGTGAGCTCTGCTTTACACCAGCCGAGTTTAAGGTGTCAGTGGGACATTGAAGTGGAACTGGGAGGTGCGGGGAGTGAGCTCTGAGCCATTCCAGGGACTGGGGATCATGCCTGGGGCACCTCCATCCCCATTTCCCTGGAATCCAGAAGAGTTGGGGGGTCCGAGCTCCCTGTACCTCAAGTGACCCTCCATCTCTCTCCCATCTCTGTCTCTCCCTGGTGTCTGTTTTTCTTCTCCTCCTCTCCTTGTCTCTCTCCCACACCCCTCCATCTCTCTCCCACGTGTCTCTCCCCTCACCTTCTCTCCCCCTCCATTTCTCTCTCCCTAATCTGTCTGTTCCCTCTGCCATGGCCCCCTTCTTCAAGCAGCCTCCCATCTTGCTCCTGCGGTCCCTCCTTCCCTGTCTCTCTCACCCCTGTTTCCACACCCTCACCTCCTACCACCCCCCTCAGCATGTTCCCTGGAAGCTGAGGGTCTCTGGGGCTCAGTCCCGGTCTCTCTCTTTCTCTCTCTCTCTCTCTGTCTCCCCGACCCTTCCCCCCAG
Seq C2 exon
CGTGTTCCCGAGGGAGCTGAAGGAGGTGTTTGCTTCGTGGCGGCTGCGCTGCGCAGAGCGAGGCCGGGAGGACATCGCAGACAGGCTTATCAGCGCCTCACTCTTCCTGCGCTTCCTCTGCCCAGCGATTATGTCGCCCAGTCTCTTTGGGCTTATGCAGGAGTACCCAGATGAGCAGACCTCACGAACCCTCACCCTCATTGCCAAGGTCATCCAGAACCTGGCCAACTTTTCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000227460-SYNGAP1:NM_006772:10
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAAACTGCGAGGTAGACCC
R:
TGGAAAAGTTGGCCAGGTTCT
Band lengths:
350-2159
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)