HsaINT0137400 @ hg19
Intron Retention
Gene
ENSG00000091428 | RAPGEF4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:HGNC Symbol;Acc:16626]
Coordinates
chr2:173883384-173885443:+
Coord C1 exon
chr2:173883384-173883530
Coord A exon
chr2:173883531-173885345
Coord C2 exon
chr2:173885346-173885443
Length
1815 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACA
5' ss Score
8.1
3' ss Seq
CATGCTTTTTATGTTCACAGAAA
3' ss Score
8.99
Exon sequences
Seq C1 exon
TTCTGTTTAAGGTCTATTGCATGGACCACACCTACACAACCATTCGGGTGCCAGTGGCCACTTCGGTGAAGGAAGTCATCAGTGCAGTTGCCGACAAGCTGGGCTCCGGGGAGGGCCTGATCATAGTCAAGATGAGTTCCGGAGGAG
Seq A exon
GTAACAGTCTTAATTCATATTTTAGGCTCTGCAAAATGGGACATTCCATCCAAGCAGAAACTATGTAAGGAGTTAGCGTGGTCATGTGAGGCTCACCCAGAGGATGAACTGGTGCTTATGTATGCTTCCACTAATAACAGAAACAGTATGGGTAGAGGTGGGTTGGGTTTCTAATGTCCCCTATCTGGTAGGTACCCACTCTAAATCAGAAAGGTGACTGGAACTGAGGACTGTCGTGTAGATGTTGGCCTGGAGTTCTTTCAATTTAAACTCTATTCAAAAAAGTTTTAGGCCTTGGAGCCCTGAAAAATATGGGCCCCAAGAGGAAATCTAGCTGGACAAGCTCAAGGCCATGGGTTTCTACAAGTCCAAAGTTGGAAGTGGTCAGAAGCTAGTTCTTTGAAGCTGATGATGGTTTTTCTCCTTACTCAGTAGAGAGGCTAGGAGCCTGGCTCAAATGAAATGAGGAATATTTTTCCTCCACGGGATTACAGTTCCTTTCACTGTCCTTGATTACATGGTGCATTTTTGAAATGTCATTTATTCGTTCATCACATATTTACTGGCCACAGTGTGGCTACGAAGGAAAGAATGAGTTAGACACAGCTCACGTCCCCAGGTTGTTCCCAGGCCAGGGAGGAGGTAGACGGTAAGTTAAAACAATTACAGTTCATGCTGGCAAGAGTTTTAGGAATGACCACATATTGTAGTGAGAGACTAGAGGAAGCAACAGTGAGGTTCATTTCTCCAGTCATGATTTGACAGCCATTTGGCGGAATCCTTCAGGAACAGGTGAGCCATTTCTGTCATGTTTTAAGGTGAATGATTCCACTGATGGAGGATTTTTAAATGCATGTTGGATTTTAAGATCTCCCTTCCATTTCTGCTCCAGTTGCACAAGGCCCAGGATGTCTGCCCTCCCTGACCCCTTGTCACCTTCCCATAGATATCCCAGGTCTCACCCTCACTTTCTTTCAGTCTTTACCCAAATGTCAGTGTCTCACTGAAGCTCCCTCCTTCATTTGCTTCATTCCCTTTCTAAAATGTTAACTTCTTCCCCTTACACAAGCTTCCTAGACCCCACCCCTGTGATATTTTTTTCTCCTTGCCTTCTCACTCTGTAATCTATTTCTTTTCTTTATTGTTGGCATCTCCCACTATGATGTAATGCTTTTTGGAGTGGGATTTTTTTTCTGTATTGTTCCCTTCTGTCTCCCCAGTGCCTGGAGCAGTTTCTGGCATGCAGTAAATACAAAATAAATGTTTATTAAATGAACTAATTTTTTAATTTTTTTGACATGTTCTCATCTGAAGAACTAATTTTTTTAATGTGGGAGGAGGCTTAATCTAGTTAATGCTATTGCCCTGCAAATTAGGGAATAAGTGAAAAAACAATAGTAAATTTTGCATCTAAAATCATGTGAGGTCTCAGAAACCTCCAAAGTTTTTAAAAAGTGATCTTTCTATGTCCAAAGTCCTGGGTGTGATTACCATCTGGAAACATAACTTGTGAGATAAATAGCCAAGTGCGGGTTTTATGTGCTCAGTAATTATGGTTGCAGCACAAAACTGGGTGAATTGACCCTCTGGCATCTCTATTCCTTTTTGTGGCCATTTCTGAAGGCATCCTGAGTGGCGCAGGGCTGCATGAATGCCGTCTTTTTTATTCCGTGGATCCCTTCAGTACTCTATTTTATGCAGTCACTCTGCGTGTTCCGGTAATTCACCAAGCTGGCAATTTGTTGGTGTGATTAGGGCAGTGCAGCAAATCTCAGATGTATTTAATAGGCAATCTCATGCTTTTTATGTTCACAG
Seq C2 exon
AAAAGGTGGTGCTCAAACCTAATGATGTTTCAGTATTTACGACGCTCACCATTAATGGACGCCTGTTTGCTTGCCCGCGAGAGCAATTCGATTCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000091428-RAPGEF4:NM_007023:22
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:
PF0078818=RA=FE(61.2=100)
A:
NA
C2:
PF0078818=RA=PD(35.0=84.8)
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:
TCTGTTTAAGGTCTATTGCATGGAC
R:
TGAATCGAATTGCTCTCGCGG
Band lengths:
241-2056
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)