HsaINT0137366 @ hg19
Intron Retention
Gene
ENSG00000079337 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:16629]
Coordinates
chr12:48135288-48137459:-
Coord C1 exon
chr12:48137313-48137459
Coord A exon
chr12:48135386-48137312
Coord C2 exon
chr12:48135288-48135385
Length
1927 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
CGCCTCTGCTGTCTTTGCAGATG
3' ss Score
11.32
Exon sequences
Seq C1 exon
TCCCCTATGACATCTGCCGGCCAGACCACTCAGTGTTGACCCTGCAGCTGCCTGTGACAGCCTCCGTGAGAGAGGTGATGGCAGCGTTGGCCCAGGAGGATGGCTGGACCAAGGGGCAGGTGCTGGTGAAGGTCAATTCTGCAGGTG
Seq A exon
GTGAGTTGTGCCCCTGGATAGACCCCAAGGGAGGGTGGCCCCTCGGATCTGCGCCCAGGTCCCCCAGTCAAGATCATTGTCATCATTGTCATCTTTCTGGTCTTCCTCAGTGTGAATGATGGCTAGCATTAATGGGAGGTGGAGTGCGTCTGTTCGAAGTGCATTTCATGCAGTGTGTAAGAGCATGAGCTCTGGAGCCTGCTGCTTGCATTCGGCACCAGCCCTTTAGCTCACCATCTGTGTGTCCTCTGGCAGGGTACTTCATCCCTCTGTGCTCAGTTTTATCATCCATAAAATGGGAATAGTAGGAGTACTTGCCTCCTGGAGGAATTGTGAGGATCAATTGAGTTCATCTATGAAAGCATTTAGAATGGTGCCCGGCACATAGTGATACATAAGTATTAGCTGCTATTATTATCATCATTTGTGTTTAGTCATTTAATATGAATTAATAACAATCTCATGAGATACAGGTACTTTTATCCTATTTTCAGACAAGAACACTGAAGCTCAAAGGGCATGAGCTATTCCTCAAGCTCACACAGTGAGAGTAGCTGGTCTTGGAACTTAAGTAGTCTTCATTTGTTTAGTCACTCAGCAAACATTTTTGAGGATCAGCTATGAGCCAGCAATATGTTAGGAGCTGGAGATACCACAGCAGGTAAAACAGGTCAGCTTGATGGTTAAGAGCATAGACGGTGGACTCCCAGACCCGTGAAGGCATCTTAGGCTCACCATTTACTAGCTGTGTGATGCTGGGCAAGTTGCTTAACCTCTCTGAGCCTGCATTTCCTCACCTGTCAGATGAGGACTGTAATTGTATCTACCCACAGGGTTGCAATGGCTAAGTGAGCTAATGTGTGTAAAGCACTTAGCACAGGGCCTGCCAGTCAGTGCTGAGAACATGGCGGGCTCAGGAGTATTAAGATGGGCCTCCAGAGAACCTGGAACATTCAAAACCACTGTTCTCTGCGGAGGGCACGGGCTTGACAGCTGGAACCCAGGGCAGACAAGAATTAGGGGCGTTCAAGAAGTGGGGATGAGAAAAGAAAAGCCTTCTCCCTTCAGGAAGTGGGGAGAGATGGTCACCTGTGTGCCCTGCCCTGGGAAGCACTGCCCTCTGCTGGCCACCTGGTGAGTTGCAGTTGCCCAAAGGTCATGTTTATTGAGACCCTACTATGTGCCAGGCACTGTTTAGAGCACTGATCTCCGAAGCACTTGGATCGACACCCATGTCAATAACCAACATTTAATTAAAACCCACACCCCACTGTGTGAATATTTGTTTGTAAGTAATACACATATATTACTACATTAATATCATAATAAAGATAGATAAAATAGAAATTGATGGAGTAGAAATGCAAAGCAGGTAGAAAAAGTAAACGTAAGTAGAAGAGCTCATATTTTCCCCAGGCACATGGATGATCTGATGTACCTTACTTTGGAGGCCACTGCTCTAGGGACTGGGGACTCAAGCACAGTCCCAGTCCATGAGGAGCTGATGAAAATCAACACCAAGGCTTATATAAGACACTTCCCAATTTTCAAAGGGCTTTTATACATAGCATGTACTTATAGCTACTATTTATATACATTATTTTATTTGACTTATGAAATAGTTGGGGCAAGTCTTATTGTCTCCATTTTACCAGGGAAGAAAGTGAGGCTGAGGGAGGCTCAGACCCTGCCCAGGTTCTTCCTGACTCACTGAGAATCTTTCCTCATCCTCTTGGATGTGCTTCCCTGGGCTGCGTGGCTGCGTGGGCACATGCACCTGTGTATTCTGAGCACCACCCAGGACTTCAACCCCGCTACTAGGAGAAACAACCTCTCAGCCTCCCAAACAGCACCTCCACCCTGGCATCCAGCTGGTCCCCGGCCTCCCTCCCTTCCCCCACCCAGTCCGCCTCTGCTGTCTTTGCAG
Seq C2 exon
ATGCCATTGGCCTGCAGCCAGATGCCCGTGGTGTGGCCACATCTCTGGGGCTCAATGAGCGTCTCTTTGTTGTCAACCCACAGGAAGTGCATGAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000079337-RAPGEF3:NM_001098531:18
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.008 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCCCTATGACATCTGCCGG
R:
ATGCACTTCCTGTGGGTTGAC
Band lengths:
239-2166
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)