HsaINT0137361 @ hg19
Intron Retention
Gene
ENSG00000079337 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:16629]
Coordinates
chr12:48141495-48141935:-
Coord C1 exon
chr12:48141857-48141935
Coord A exon
chr12:48141646-48141856
Coord C2 exon
chr12:48141495-48141645
Length
211 bp
Sequences
Splice sites
5' ss Seq
CCAATATCC
5' ss Score
-12.74
3' ss Seq
TTCCCTTGACTGGTGCCCACCTT
3' ss Score
-5.98
Exon sequences
Seq C1 exon
AGACATTCCTCAGCGACTTCCTCCTGACCCACAGGGTCTTCATGCCCAGCGCCCAACTCTGCGCTGCCCTTCTGCACCA
Seq A exon
ATATCCTTCCAGCTCCAGGGGGATGGTGTGCATGGGGATAGGATGGTGCGTGGGGTTGAGAGAAAATCTCACCAGCGTGGCTGTGCTGAGCCCTTTAAATGCCAGCCTGCTGCCAGGCCCAGCTTGCCAGGGGCCCTGGGCATCCTGCCCCTCCTTTGCCTCAGGTGGGTGGCCCTGCTTGGATGTTGTGGTTCCCTTGACTGGTGCCCAC
Seq C2 exon
CTTCCATGTGGAGCCTGCGGGTGGCAGCGAGCAGGAGCGCAGCACCTACGTCTGCAACAAGAGGCAGCAGATCTTGCGGCTGGTCAGCCAGTGGGTGGCCCTGTATGGCTCCATGCTCCACACTGACCCTGTGGCCACCAGCTTCCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000079337-RAPGEF3:NM_001098531:13
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.081
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=FE(23.6=100)
A:
NA
C2:
PF0061815=RasGEF_N=FE(45.5=100)
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:
AGACATTCCTCAGCGACTTCCT
R:
CTGGAGGAAGCTGGTGGCC
Band lengths:
230-441
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)