HsaINT0137384 @ hg19
Intron Retention
Gene
ENSG00000079337 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:16629]
Coordinates
chr12:48151649-48152244:-
Coord C1 exon
chr12:48152155-48152244
Coord A exon
chr12:48151862-48152154
Coord C2 exon
chr12:48151649-48151861
Length
293 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGTG
5' ss Score
4.58
3' ss Seq
CTTTCCTCCCCGTGTCACAGGTG
3' ss Score
10.28
Exon sequences
Seq C1 exon
GTTAGTCAGGGCTGAGGAGGAGAGGAGAAGGGTTTAAGCCGAAGCTGCATTTCTGGGAGACCTAGTGAATCTATAGCTTCATACTGGGAG
Seq A exon
GTAGTGGAGATCCCTGCAGGGGCATGGGCAGTGAGATGGGACAGAATTCCAAAGAGGACTAAGAAGGGCCTGATCTTTTCCAAGAGCCAGCTGGAGACCCCTAAGTGCGCCAGACCGGCAGGCCCCAGTGAAGGTCTTCCTGTTCCTCCCCCCAGCTCCTGGCAGGGTTGCAGCACCTCCGCCTGACCAGTCCAGAGGACTCTAAGGAAGTAGTTCTGCCTGGGGCAGTTGTACTGTGGCCCAGCCGCCCCAGTCGTGTCCCATGGCTGTCCACTTTCCTCCCCGTGTCACAG
Seq C2 exon
GTGGGCTGGCCAGGTGAGAGCTGCTGGCAGGTGGGCCTGGCTGTGGAGGATAGCCCAGCTCTGGGAGCACCGCGGGTGGGAGCCCTCCCTGACGTGGTGCCGGAGGGGACACTACTCAACATGGTGTTGAGAAGGATGCACCGGCCCCGAAGCTGCTCCTACCAGCTGCTGCTGGAGCACCAGCGTCCGAGCTGCATCCAGGGGCTGCGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000079337-RAPGEF3:NM_006105:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.017
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTAGTCAGGGCTGAGGAGGA
R:
CCCTGGATGCAGCTCGGA
Band lengths:
293-586
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)