HsaINT0137318 @ hg19
Intron Retention
Gene
ENSG00000107263 | RAPGEF1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:HGNC Symbol;Acc:4568]
Coordinates
chr9:134464188-134465363:-
Coord C1 exon
chr9:134465273-134465363
Coord A exon
chr9:134464374-134465272
Coord C2 exon
chr9:134464188-134464373
Length
899 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TGTGCTCTTTTGTCCTTCAGCCT
3' ss Score
9.03
Exon sequences
Seq C1 exon
ATGAGAAATTCTCTCCCTTTGCCGACACATTCAAGAAGCGCGTCAGCAAGAACACGTTCTTCGTGCTGGTACGGGTGGTGGATGAGCTCTG
Seq A exon
GTGAGTGCTTCACCCTTGGGGTCCTGGGGGCCAGTGGGGAGGCAAAGGCTCCATTCCACCTGCTTCTCCTGCCCATCGGCTCTGGGCAGAGCTGGCTCTTGCCTGCTCTATCTTGGTCCTTTGAGAGAATGGCCTGTGCCCGATAGACCAGGGTGAGATGGGTGAGGTGTCTCTCCACCCTGCACCCAGGCCCTGGATTTCCTCATGAGGTCCCTCCTGGACCCTCAGGAGAGAACCCGCCCAACGCACCTGCTCCCATGGTATCTTAGGTCCAGTCTCCAGCAGGCCGTGCTCTCAGCCGCCAGCCATGGTGGAGGCTGTGTGGAGGCTGGAATGGGAGAGGCCACCTCTCCCTCGCTCCTCAGTGTTTCCATGGCTGGCCATCTGACAGCATGGCACTTGGCCATATCCGTTCCGCTAACAAATCTCCATCAGGCGGACTGCCTTCCTCCTGCTGGGGGAGATGACCATGGTAAGTGGCTGTGCGGCTGGGAAATGGCCACGTGTGGACAGTGCTCAGCAGGGCAAGTTGGGGAGCATCTAGTCTGAGAGGCCGGGAAGTCTTGGTGTCTCATTGCCCAATGGGAGCAGCAGCTCCCCAGGGCGGGATTCGTGTAGGACTTGTCCCTGCAGCCCAGGCCCCAGCACAGTCACTGGCGCTTGTCCAGCGCCAACAGATGGCTGTTGAGTGTGTGGCAGGTGCTTGTGACCATCCCAACACCTCCAAGGACACAGGCAGCCATCCCAGGCTCTCGTCTCCTGCTCTCTTCCCATGAGAAATTTCCCAGCCAGCTCTGTGCCGGTCACAGCCCCGTGCCCTTTGTGTGTCTCAAGGCAAAGACAGACTCTGCCTGGGCCTTGCGTTCCTGCTCCTCACCTTGTGCTCTTTTGTCCTTCAG
Seq C2 exon
CCTGGTGGAGTTGACAGAAGAGATCCTGAAGCTGCTGATGGAACTGGTCTTCCGCCTGGTGTGCAATGGGGAGCTGAGCCTGGCCCGTGTGCTCCGGAAGAACATCCTGGACAAGGTGGACCAGAAGAAGCTACTCAGGTGTGCCACCTCCAGCCAGCCCCTGGCAGCCCGGGGGGTAGCAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107263-RAPGEF1:NM_005312:16
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:
PF0061815=RasGEF_N=FE(31.0=100)
A:
NA
C2:
PF0061815=RasGEF_N=PD(20.0=31.7)
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:
GAGAAATTCTCTCCCTTTGCCGA
R:
CTGGCTGGAGGTGGCACA
Band lengths:
246-1145
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)