HsaINT0137383 @ hg19
Intron Retention
Gene
ENSG00000079337 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:16629]
Coordinates
chr12:48143173-48143600:-
Coord C1 exon
chr12:48143524-48143600
Coord A exon
chr12:48143320-48143523
Coord C2 exon
chr12:48143173-48143319
Length
204 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
AGACTGAGGCCTGGCTGCAGGGG
3' ss Score
-0.92
Exon sequences
Seq C1 exon
TGTTCAGCCAGGGGGACAAGGGCACTTCGTGGTACATTATCTGGAAGGGATCTGTCAACGTGGTGACCCATGGCAAG
Seq A exon
GTGAGCCCTCCCTCCTCCCCACCCCAGTGCCCTGGGTCCTAACTGCTCCCTGGTCCATGTCCTCATGGGCAGTGCCTTTGTTGATCTACTGCTGCTGACCCCGTGTCTCCTGTGTGGGTTGTTCTCCTGCCGTGGGTCTGTCCTGGCAAGAGCTGGGGGCGGCAGGGGCGGCAGGGGCGGGCTGAGACTGAGGCCTGGCTGCAG
Seq C2 exon
GGGCTGGTGACCACCCTGCATGAGGGAGATGATTTTGGACAGCTGGCTCTGGTGAATGATGCACCCCGGGCAGCCACCATCATCCTGCGAGAAGACAACTGTCATTTCCTGCGTGTGGACAAGCAGGACTTCAACCGTATCATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000079337-RAPGEF3:NM_001098531:9
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:
PF0002724=cNMP_binding=FE(29.4=100)
A:
NA
C2:
PF0002724=cNMP_binding=FE(56.5=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:
TGTTCAGCCAGGGGGACAAG
R:
TGATGATACGGTTGAAGTCCTGC
Band lengths:
222-426
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)