HsaINT0137482 @ hg38
Intron Retention
Gene
ENSG00000108352 | RAPGEFL1
Description
Rap guanine nucleotide exchange factor like 1 [Source:HGNC Symbol;Acc:HGNC:17428]
Coordinates
chr17:40188866-40189375:+
Coord C1 exon
chr17:40188866-40188978
Coord A exon
chr17:40188979-40189207
Coord C2 exon
chr17:40189208-40189375
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:ENST00000613811:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.089 A=NA C2=0.001
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
Chicken
(galGal3)
No conservation detected
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