HsaINT0137415 @ hg19
Intron Retention
Gene
ENSG00000091428 | RAPGEF4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:HGNC Symbol;Acc:16626]
Coordinates
chr2:173830290-173832172:+
Coord C1 exon
chr2:173830290-173830411
Coord A exon
chr2:173830412-173831988
Coord C2 exon
chr2:173831989-173832172
Length
1577 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
TGCTTCCATGTTTCCCATAGTGG
3' ss Score
7.02
Exon sequences
Seq C1 exon
ACAATGCTGTGTGGGAACTGAACTGGTGGACTGGATGATGCAGCAGACACCATGTGTTCACTCCCGGACTCAAGCTGTTGGCATGTGGCAAGTCCTGTTAGAAGATGGTGTTCTCAACCACG
Seq A exon
GTAAGATGAGCCCCAGTCCCTGGAAACCTCTCAAGAAATGCTAAGTGCATTTCCCTGGGTAAGTAGTTGCTGAACTCTTGAATGGGCAAGAAAGAATTACGATCCCTTTAGGGACCTGCAGAGCTAGCATCTTCATTTAGCAATACAAATGCAGCAAGTAGATGCTATTGATTGCTATGTTCCACCATTGTACCTTCCTAACTTGGGAGAATGTATGAAAGGAAAATGAAATTGCAGCCCGAGTGCATCAGTTCCAATTATGTTTATTAGTTTGCATTCACGGTTCATTGATAGCGTGATTATACTCTGAGCAGTGCATAGCAATCCTGATGCAGGGGCAGAATGAAGAGCAGTGAAGTGTGTGGCTGGGCTGATGACATGAAAGTAAGTAATGAATTCGGAAGCTGCCTTTTAATTGTGCCGCTGTCTGGGAGAGCCAATTTGTATACCCACAGGATGACCATATTTAAAATCAAGAATGTGCTCTGCAATTGTGGCTCTTGATAACTGCAGGGGCTGTAATTGAACAGAGTAGCTCTTCAGGACTGGTGTGTAACTCTGGCCAAACTCTTATGCCATTTGTTTAAGACACTTCCAAACAGACAAAATATTAAAAACATTCATTTCATTTACCAACACCTGGGAATCTAGTAATGGTTTTGCCAGCGTTTCTCATACTTTAATGTGCATACATGTCACCTGGGACTCTTGTTAAAGTGCAGATTCTGATGTAGCTCGTCTGGAATGGACTTAGAGTCTGTATTTCCAACAAGTTCCCAGATGCTGCTGCTGCTGCTCCTCCAGGAATCGCCCTTTGAGCAGCAAGGGATCTACTGCTTGTCTTTACCTTTTGAGAGTATTGATGCTCCATCCTGAAAAGGGGCTCAAGGCTGTAAGACATGTACATGAGGGATTCTGAGCCACGTTCATTGTCTTTGTCCTACCGAGATTTAAATCCTGTTTAAAGGAACAAGAGGAAAAAACTTTAAGACATCAGATTTGGAAGAAAATTACCACAAAATCCTTCTAGCAGTATATGATCTAGAAACCTGGTCTGGTCAGCTTTGTTCAAACAACTAATTTTATACTAACATTTTTTTCCAGAGTGCAGACAGTACAGTTGATAAACAGTACATATAGAAAGAATAACATAAATTCTGATCCTGACAAGGCAGATTGTTTTCAAAGCCTGTACTTTCCAAAGCTGTGACAGAACATGACCTGGCAGTTGGTTCCTTTCCTGTTTGGGACACAGGTCCCACATCCTAGAAAATATCAGGAAGACGATTTCTGCAGGTCAAAGTGTTCATCTGAGAAATGCTGGCAGGTCCTCAAAGGGAGTCCCACAGAGGCCGAGGAGATGGGTGGGTCAGAGAGGGCTGTGGTGTGCATGACTGCAGCCCCGAGGTCATGTCTTCCAGCTGCACAGTCTGGGCAGGGCAGAGTGAGAAGGGCGAGGAGGCTCCCGGCTTTGCTGCCACTTGGCCCTCCTGCCTGACACTCTGCATTTGTTTCTAGTAAACGGAGCTGTGAGGCCGAGGTGCTGCAGCTGACACGTGCTTCCATGTTTCCCATAG
Seq C2 exon
TGGACCAGGAGCACCATTTCCAAGACAAATATTTATTCTATCGATTTCTGGATGATGAGCACGAGGATGCCCCTTTGCCTACTGAGGAGGAGAAGAAGGAGTGTGATGAGGAGCTCCAGGACACCATGCTGCTGCTGTCACAGATGGGCCCCGACGCCCACATGAGGATGATCCTTCGCAAACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000091428-RAPGEF4:NM_007023:9
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=0.226
Domain overlap (PFAM):
C1:
PF0061016=DEP=FE(57.7=100)
A:
NA
C2:
PF0061016=DEP=PD(21.1=24.2)
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:
ACAATGCTGTGTGGGAACTGA
R:
GATCATCCTCATGTGGGCGTC
Band lengths:
295-1872
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)