HsaINT0137323 @ hg19
Intron Retention
Gene
ENSG00000107263 | RAPGEF1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:HGNC Symbol;Acc:4568]
Coordinates
chr9:134459698-134459983:-
Coord C1 exon
chr9:134459905-134459983
Coord A exon
chr9:134459800-134459904
Coord C2 exon
chr9:134459698-134459799
Length
105 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
CACCGCCCCTCTCTCGGCAGCAC
3' ss Score
9.31
Exon sequences
Seq C1 exon
GGTCCGGTCCATAATCATGTTACAGGAAAAGGCCCAGGACAGGGAACGGCTGCTCTTGAAGTTCATCAAGATCATGAAG
Seq A exon
GTAATGGTGGCCAAGTCCTTCCCAGGCCCCCATCATCAGTCCCTGCTCTGGGAGCCCGGGACCCGCCTGCCCTCCTGCCTCACGGCACCGCCCCTCTCTCGGCAG
Seq C2 exon
CACTTGCGGAAGCTGAATAACTTCAACTCCTACTTGGCCATCCTCTCTGCCCTGGACTCGGCGCCCATCCGCAGGCTGGAGTGGCAGAAGCAGACTTCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107263-RAPGEF1:NM_005312:20
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=FE(14.6=100)
A:
NA
C2:
PF0061714=RasGEF=FE(18.5=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:
GGTCCGGTCCATAATCATGTT
R:
GAAGTCTGCTTCTGCCACTCC
Band lengths:
177-282
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)