HsaINT0137371 @ hg19
Intron Retention
Gene
ENSG00000079337 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:16629]
Coordinates
chr12:48133924-48134178:-
Coord C1 exon
chr12:48134088-48134178
Coord A exon
chr12:48133975-48134087
Coord C2 exon
chr12:48133924-48133974
Length
113 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
CATCTGCCTCCTTTTCACAGCGG
3' ss Score
9.7
Exon sequences
Seq C1 exon
CCTCAAGGAGCAGAAGAATCTCAATTCCTTCTTTGCCGTCATGTTTGGCCTCAGCAACTCGGCCATCAGCCGCCTAGCCCACACCTGGGAG
Seq A exon
GTAAGTGTGGTCTGGAGGGCCCCCTCCTGAGGTCAGGCCTCAGGCCCTCCTGGGAGTGCTGGATGGGGCTGGGCCTCCCCCAGAGCAGCCGCTCATCTGCCTCCTTTTCACAG
Seq C2 exon
CGGCTGCCTCACAAAGTCCGGAAGCTGTACTCCGCCCTCGAGAGGCTGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000079337-RAPGEF3:NM_001098531:22
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=0.000
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=FE(22.4=100),PF136131=HTH_Tnp_4=PU(69.7=74.2)
A:
NA
C2:
PF0061714=RasGEF=FE(12.7=100),PF136131=HTH_Tnp_4=PD(27.3=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCAAGGAGCAGAAGAATCTCA
R:
CTCTCGAGGGCGGAGTACAG
Band lengths:
135-248
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)