HsaINT0137332 @ hg19
Intron Retention
Gene
ENSG00000107263 | RAPGEF1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:HGNC Symbol;Acc:4568]
Coordinates
chr9:134503300-134504059:-
Coord C1 exon
chr9:134503936-134504059
Coord A exon
chr9:134503484-134503935
Coord C2 exon
chr9:134503300-134503483
Length
452 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
TTTTTCTTTTTCCACTTGAGGAT
3' ss Score
7.6
Exon sequences
Seq C1 exon
TCCTCCACCAGCATTGCCACCCAAGAAAAGACAGTCGGCGCCGTCCCCTACCCGAGTGGCTGTGGTGGCCCCCATGAGCCGAGCCACCAGTGGCTCCAGTTTGCCTGTTGGAATCAATAGGCAG
Seq A exon
GTAATGCAGCCCCTGTTCCCTGCATGGGAAGGCAGGGAGGGGGTGGGGGGCTCAGGGATGTGGCTCCTGAAGCTGAAAGAAACCCATGGTCTTCAGGCGCTGGTGTTTGTCACATCGAGGAGTGCGAGACCTTGTACCCATCCCTCTCTCTCCAGGACACGGTCCAAGTTCCCATATGGGGATAAGGGTCAGGGCAGGGAGGGCAGAGCCAAAGGGCGTCTCCTGGGGATAGGTGAGTCCAGCCCCAGGGCCCTCCCTGGCCACACCCCCCACAAACTCCAGATGGCTGCTTCTCAGCTGTATGTGTCCTTCGACTACTGACGTCAGAGGTGGTTTCTGAGTTCGCCTGGCAGTATTTCCTTCTCTAAGTAAATGCACCGGTTGCCTCACCCCTGGTCTGTGCCACCGTTTCTCAGAAGTGATTTGGCTTTGTTTTTCTTTTTCCACTTGAG
Seq C2 exon
GATTTTGATGTTGACTGTTACGCACAGAGGCGACTGTCAGGAGGCAGCCACTCATATGGTGGAGAGTCGCCCCGCCTCTCCCCCTGCAGCAGCATAGGCAAGCTCAGCAAGTCAGACGAGCAGCTGTCCTCTCTGGACAGGGACAGTGGGCAGTGCTCCCGGAACACAAGCTGTGAAACACTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107263-RAPGEF1:NM_005312:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.895 A=NA C2=0.796
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:
CACCAGCATTGCCACCCAAG
R:
CACAGCTTGTGTTCCGGGAG
Band lengths:
294-746
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)