HsaINT0137320 @ hg19
Intron Retention
Gene
ENSG00000107263 | RAPGEF1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:HGNC Symbol;Acc:4568]
Coordinates
chr9:134463123-134463413:-
Coord C1 exon
chr9:134463329-134463413
Coord A exon
chr9:134463218-134463328
Coord C2 exon
chr9:134463123-134463217
Length
111 bp
Sequences
Splice sites
5' ss Seq
GAGGTACAG
5' ss Score
6.62
3' ss Seq
TGCCTTCTTTCCTTTTGTAGATT
3' ss Score
12.39
Exon sequences
Seq C1 exon
GCCGGGGACCTTGCACGACTTTCACAGCCATGAGATAGCGGAGCAGCTAACGCTGCTGGATGCTGAGCTCTTCTATAAAATAGAG
Seq A exon
GTACAGGCTGCTCCTGCCAGGGGGAGCCACACTGTTTGTCCCTGAATGAGAGAAACCCCCATCAGGGGAAAGCCGGGGCTCCACCTCCATCTGCCTTCTTTCCTTTTGTAG
Seq C2 exon
ATTCCTGAGGTTTTGCTTTGGGCAAAAGAGCAGAATGAGGAGAAGAGCCCCAACTTGACCCAGTTCACGGAGCACTTCAACAACATGTCCTACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107263-RAPGEF1:NM_005312:18
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.094
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(12.9=79.3)
A:
NA
C2:
PF0061714=RasGEF=FE(17.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACCTTGCACGACTTTCACA
R:
GGACATGTTGTTGAAGTGCTCC
Band lengths:
170-281
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)