HsaINT0137399 @ hg19
Intron Retention
Gene
ENSG00000091428 | RAPGEF4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:HGNC Symbol;Acc:16626]
Coordinates
chr2:173882154-173883530:+
Coord C1 exon
chr2:173882154-173882232
Coord A exon
chr2:173882233-173883383
Coord C2 exon
chr2:173883384-173883530
Length
1151 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TTGTTACTGCCTTTGGATAGTTC
3' ss Score
5.84
Exon sequences
Seq C1 exon
CACAAGGTTCTTTTGCAACAGTTCAATACGGGCGATGAGAGAGCCCAGAAGCGCCAGCCTATCCGCGGCTCTGATGAAG
Seq A exon
GTGAGAACCCTCTTCCAACTAACTCGTAGTTGTATAGATTATTTAGTCAGGATAATGGTAAGCATCACCTTGGACCCACAGAATAGCTTCTTTTGAAGATGCCCTGTTGCCCTCCAGATGGTTTGCTTGGAGGTGCCCTTTGGTGGCCCGATTATTTATGTCCTTAAACTCTTGTGCCTGAAGCCGAGATGCCTGTCTACCTTTCCCTGATTTGGCCTCTCCCTGCTTAACCCCTTTCCTTGGAGGAAATGAAGATGATCTCAGGGCCTGGTTGTCAGGATTGCCCACCCCTGGGAAAAGCTGGTGGGAAGGTAGCTGGCGCCTAGTGGGTGCCAAGGAGACAATGGATCACCAGCATCCTGCCCAGGGACAATGCTCTGGCCCTGAGCCCAGCCCTGAGCAGGGAGGCTTTACATCAGGAAGATCAAGATGCTGGCTTTTGTTTGGTTATTTAAGATTCTCCAAAGAATCACAACCAAAAATAGTCACAATAATAATGATAAAAATTTCATTTAAAGCTATAAATAAATCTTGTCATTTAGGACTGCCTCTAAACCCAGGAATTATAATATAATAATGGGAATTGCTCCCAGGATTTTTGTGTTCAGAGTTGAGCCTCTGGGTGCCATATCCAGATCTGCTGATCTAAGTCTGCTGAGCTAAATAGCATCCGAGCTTACATGGCCTGGCCCCAAAGCACACAAGCCACTGAAGCAAGTGAGCAGGAGTGTCAGCACGTGCTCATGGCCCAGGCGGAAGCCCTCCTGTGTGCAGAGAGGTGAATGGTGTCTCCCCACTGCCACACAGGGTAGCAGTGATCTGTGAATTGCCTACAGTATAGCACTTCAGACCCTGAACATCAGCCTGAAGATACTCTCAATTTTTTCCCATGACCTCTTTGTGGGGTTTTCACCAATATCTCTTGTTCTTTTAATTGGACTTGGCAACCATATGTGCACCTATTCTTAGACCAATGCTAAGGTAAGCAGTTTAGAAGGGGCAGGAATAGGGGTAAATGAGTATGAATAAATACAGTAACAAAAATGGCAAAATGATGCAAATTGGAGAGGATGCCTAAACATTTTTCATAACTATAGTTTTATTGAAAACTCTTAAGAGTGATTTACTACCTTGTTACTGCCTTTGGATAG
Seq C2 exon
TTCTGTTTAAGGTCTATTGCATGGACCACACCTACACAACCATTCGGGTGCCAGTGGCCACTTCGGTGAAGGAAGTCATCAGTGCAGTTGCCGACAAGCTGGGCTCCGGGGAGGGCCTGATCATAGTCAAGATGAGTTCCGGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000091428-RAPGEF4:NM_007023:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.148 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0078818=RA=PU(2.5=7.4)
A:
NA
C2:
PF0078818=RA=FE(61.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACAAGGTTCTTTTGCAACAGT
R:
TCCTCCGGAACTCATCTTGACT
Band lengths:
225-1376
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)