HsaINT0137359 @ hg19
Intron Retention
Gene
ENSG00000079337 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:16629]
Coordinates
chr12:48142237-48142714:-
Coord C1 exon
chr12:48142602-48142714
Coord A exon
chr12:48142326-48142601
Coord C2 exon
chr12:48142237-48142325
Length
276 bp
Sequences
Splice sites
5' ss Seq
CCGGTAATA
5' ss Score
5.56
3' ss Seq
AGATTGGCCATTTCTGCTAGGTA
3' ss Score
4.56
Exon sequences
Seq C1 exon
GATGTGGAGGCAAAGACCATGCGGCTGGAAGAACATGGCAAAGTGGTGCTGGTGCTGGAGAGAGCCTCTCAGGGCGCCGGCCCTTCCCGACCCCCAACCCCAGGCAGGAACCG
Seq A exon
GTAATACACCTGCCATGCTCCCTCTCCACACTGTCCCTCCTTTCATTTCCCAATCTTTGCTCCCTTCCCCTGTGTCATATCCCTGCCCTCTGGCCACTTGTGGATGGAGAGGTATTGAGGGACCAGGATGTGCCTGCTGAGCCAGTCTCCTCCCTGCCCTAAGGTGGGACAGGGCTGGCTAATGGAGAAAAATGATGTAATTGATTATTGATGTCTGCCCAGGTGTGGGAGTGGGGAGTAGTGGCACCAGTGCCAAAGATTGGCCATTTCTGCTAG
Seq C2 exon
GTATACAGTGATGTCTGGCACCCCAGAGAAGATCCTAGAGCTTCTGTTGGAGGCCATGGGACCAGATTCCAGTGCTCATGACCCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000079337-RAPGEF3:NM_001098531:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.474 A=NA C2=0.161
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(2.4=5.3)
A:
NA
C2:
PF0061815=RasGEF_N=PU(25.5=90.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGTGGAGGCAAAGACCATGC
R:
CTGTTGGGTCATGAGCACTGG
Band lengths:
201-477
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)