HsaINT0137322 @ hg19
Intron Retention
Gene
ENSG00000107263 | RAPGEF1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:HGNC Symbol;Acc:4568]
Coordinates
chr9:134525516-134526336:-
Coord C1 exon
chr9:134526197-134526336
Coord A exon
chr9:134525630-134526196
Coord C2 exon
chr9:134525516-134525629
Length
567 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGC
5' ss Score
7.31
3' ss Seq
CCAGGTTTCCTCTCTTCCAGGAG
3' ss Score
9.2
Exon sequences
Seq C1 exon
ACTCTCAGCGTTCTCATCTCTCTTCCTTCACCATGAAGCTGATGGACAAATTCCACTCACCCAAAATCAAGAGAACGCCATCAAAGAAGGGAAAACCAGCTGAGGTGTCCGTAAAGATTCCAGAGAAGCCTGTGAACAAA
Seq A exon
GTAAGCTGACTCTGGATGTTTCTCCTGGCCTCACCTGCTTCCAGCAATATGAGTTTGTGCGATTTGTATGTTCCCTCCCTGGGGATTGAGCTTTCAGTGCATCATACCTACTTCGTAGCATTCCATGGGCGGGACCTTTGGTGTCCTTGTAAAATAAGAACCATTAGGATGGTGAGTGTTTGCCACGTTAGCCAAGCTCAGTTGGCTAAGACAGTTCTCCTTTTCCAGCTGTGTCATCCTCTGGGCATTTAAAACAGCTCAGCACATCATGTCCACACCCCAGGCTGCTGCCTCCCTGCCCTGCAGTTCCCTACGTTGCCTTGGCGCACACTCAAACACAGGGAACTCTGTGATGTCCAGAACATCCATCATTTGGCTTTAGGGCCTGTGCTCTGAAACATGCAAACCCCTTGAGACACAGCCAAAGATGTCCTCAAGAGTTAGTGGCCTCAGCAGGGCCAGTCAAGCCAGATATGTTGAAACAGCTATTGACTTTCATCAACCCCTCCCTTCGGCCTCAAACAGCCATTTCAAACTCTGTAGGAATCCAGGTTTCCTCTCTTCCAG
Seq C2 exon
GAGGCAACAGACAGATTTCTACCAGAGGGCTACCCTCTCCCCTTGGATCTGGAGCAGCAGGCAGTAGAATTTATGTCCACCAGTGCTGTGGCTTCCAGGTCTCAAAGGCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107263-RAPGEF1:NM_005312:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.551 A=NA C2=0.105
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
ACTCTCAGCGTTCTCATCTCTCT
R:
CTTCTGCCTTTGAGACCTGGA
Band lengths:
254-821
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)