HsaINT0137365 @ hg19
Intron Retention
Gene
ENSG00000079337 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:16629]
Coordinates
chr12:48137313-48137851:-
Coord C1 exon
chr12:48137770-48137851
Coord A exon
chr12:48137460-48137769
Coord C2 exon
chr12:48137313-48137459
Length
310 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGT
5' ss Score
8.46
3' ss Seq
CAGTCTGGTCTCCTCTTCAGTCC
3' ss Score
5.93
Exon sequences
Seq C1 exon
GCCCGGAACTTGCCTGTTTGGCTCCCCAACCAGGACGAGCCCCTTCCTGGCAGCAGCTGTGCCATCCAAGTTGGGGATAAAG
Seq A exon
GTTGGTGGTCTGTGCCGGCTGGGCACAGCCCGACATCTGCACCCTGCTGTCTCTGCCTCTCTTGTCCTGCTGTCGTCACTCTTGACCTCGGTGTGCCTGGGCCAAGGTGGCACGCTGTACTCCTCAGGGTCTGTGTTCCAGGCTGCTGGCTAGATCTGCCTCCTACCTGCCTCTTTTTTGCTCAGGGCCTCCCCACCTGCAGCTCAGCCTCTTGGGGATCCCTCCCACCATTACTGCAATAGCCGCCCTCTCCCTCCTGGGGTGGAGATCAGGCAGCCCTTCCCACAGCTCAGTCTGGTCTCCTCTTCAG
Seq C2 exon
TCCCCTATGACATCTGCCGGCCAGACCACTCAGTGTTGACCCTGCAGCTGCCTGTGACAGCCTCCGTGAGAGAGGTGATGGCAGCGTTGGCCCAGGAGGATGGCTGGACCAAGGGGCAGGTGCTGGTGAAGGTCAATTCTGCAGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000079337-RAPGEF3:NM_001098531:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.250 A=NA C2=0.008
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CCCGGAACTTGCCTGTTTGG
R:
ACCTGCAGAATTGACCTTCACC
Band lengths:
227-537
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)