HsaINT0137482 @ hg19
Intron Retention
Gene
ENSG00000108352 | RAPGEFL1
Description
Rap guanine nucleotide exchange factor (GEF)-like 1 [Source:HGNC Symbol;Acc:17428]
Coordinates
chr17:38345118-38345627:+
Coord C1 exon
chr17:38345118-38345230
Coord A exon
chr17:38345231-38345459
Coord C2 exon
chr17:38345460-38345627
Length
229 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
ATTTTCCTGTTTCCGTCCAGTCT
3' ss Score
7.78
Exon sequences
Seq C1 exon
GATTCCAGAGGAGAACCAGCCACCCAGCAAGCAGGTGAAGCCACTCTTCCGCCACTTCCGCCGGATAGACTCCTGTCTGCAGACCCGGGTGGCCTTCCGGGGCTCTGATGAGA
Seq A exon
GTGAGTGTGGGCATTAGGAGGGGCAGGGTGTCCTGAGTGGCTCAGGGGGACATATCTCTGGGTCTTGAGCACCCTCAGTGGCATCTCCCTGGGTGGTAGAACCAGCCCCTTTCACAGGACCTTCTTCAGAGGCCAGCCTCTGGTGGGGAATAGAGGCACCCTGGAGGAGACTGTGCCAGCTGCTGCCACTCTGCCCTCTGTTGAAAGCCATTTTCCTGTTTCCGTCCAG
Seq C2 exon
TCTTCTGCCGTGTATACATGCCTGACCACTCTTATGTGACCATACGCAGCCGCCTTTCAGCATCTGTGCAGGACATTCTGGGCTCTGTGACGGAGAAACTTCAATATTCAGAGGAGCCCGCGGGGCGTGAGGATTCCCTCATCCTGGTAGCTGTGTCCTCCTCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108352-RAPGEFL1:NM_016339:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.083 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0078818=RA=PU(2.6=5.1)
A:
NA
C2:
PF0078818=RA=FE(71.8=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:
ATTCCAGAGGAGAACCAGCCA
R:
CAGAGGAGGACACAGCTACCA
Band lengths:
277-506
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)