HsaINT0137324 @ hg19
Intron Retention
Gene
ENSG00000107263 | RAPGEF1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:HGNC Symbol;Acc:4568]
Coordinates
chr9:134457992-134459799:-
Coord C1 exon
chr9:134459698-134459799
Coord A exon
chr9:134458090-134459697
Coord C2 exon
chr9:134457992-134458089
Length
1608 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
GTCCTGTCCTGTCCTGCCAGGGC
3' ss Score
9.84
Exon sequences
Seq C1 exon
CACTTGCGGAAGCTGAATAACTTCAACTCCTACTTGGCCATCCTCTCTGCCCTGGACTCGGCGCCCATCCGCAGGCTGGAGTGGCAGAAGCAGACTTCAGAG
Seq A exon
GTGAGTGGCCTTGGGGCGTGGGCGGGAGGGTGGCTGGTAAGGGGGGCCGCCCAGCCCTCAGGCGACTAGCTGTGGCAGAAAGTGCTCCCACTGGAGCAAATGCTGGGCCTAGGCCCCTGCTCTGCCACCGACATGCTGTGTGACCAGAACAGCTGCCCTCCCGCCTTCCTGTCTCTGATCCCCAATCTTCAGGCCCCCGGGAGCTTCGAGGTTGGTTCTGGGGTGGTCACATCCCGGTGTTCTGCTGCCACCCAGCAGGCCCATCCCTGGGTTCCCGCCTCCCCCGCCCGCCCTCAGCCCGTTCTTCTGAAGGGTCTGCTTCGGGCCGGGCACTGCGGTAGGTGCTGGGGACGCACTGTGAACAGCCCAACATGATGTTGGGTGAGTTTCTGCTAGATAAGCACTAAAAGAAGAAGGGTGGGCAGGTGGGCCAGCCCAGAGGAAGTGTCACTCATGCCACCATCTGCAGAGGAGGAGGAGTTTCCTGGGAAGGGAAGAGAATCAAAGGGGACAAAGGAGTGCACAGCCAGGAGCAGGTGGGGGTCAGCACCTCCAGGGACAGGAGGAGGCCAGGGGACCACATCCCGGGAGAAGGGGACCAGTTCTAGGTCATGAGAGCCTCAGGAGCCTGGTGAGGAGTTGGACCTTTATCCTGTGTAGGGAAATAATATTGCAAATGGGGGCAAAACCCATGGCTTTTGAGTGTCAGCCAGGCCACCCAGGGGTCATGTCAGGGACCCAAGTTCAGCCAGGCCACCCAGGGATTGTGTCAGGGACCTGAGTGTGACCAGACCACCCAGAGGTCATGTCAGGAACCCGAGCGTCAGCCAGGCCACCTGGGGGTCGTGTCAGGAACCCGAGTGTGACCCAGGCCACCCAGGGGTCATGTCAGAGACCCGGGTGTCAGCCAGGCCACCCAGGGTCTTCTTGTTCAAGCCCATGTTCAGGGATGGTTGTAAGCTAGTGTATGGGGAGAGGTGGGAAATTCACACGGCCTCTGCATGGGGGGTCCTCAGGAGGCAGCACTTCAGGGAGAGGCACGTAACAGGAGAAGAGGCAGGAGAGGGGCCTTCTGAGTGGGGCAGGGCTGGCTGAGTCTCCTAGGTGGGAGCCCCCCACCCCTGCAGGAGAGAAGCCACCCAGCCCTGGGGAGGGCGAGGTCACATGCTATCTTTAGTTGGTCCTCCCTGAGTACAGGGCAGAGCAAAGGCAGCTCCGAGTCAGGAGTGACGCCACTCAGTGTGTGCCTGGGAAGCTCCTCTGGCTGCACCGCCGAACAGGGCCAGGCAGGAGCCCATCTTCCGGGATGTCGTATACACACAAGCGCTGGCTGCCCAGGCACAATGAGTACTGTGGGGTGTTTCTCCACAAAACGGCCTGAAGTCCCCTGTGACCAGGGGTTGGGCTGACACTCGTTGAAAAGGACAGAATCCCTGCTGGCCAGGGCCAGGACCCACACCTGGCTGGGTGTTTGTGCGTAGTGGGACCTGTGGAGTTGGGCAGAGGGTGGTTGACCCTCCAGTTAGTGAGGAGGACCAGGGCTCTGCCCCAGCATTGCCCCAGCACTCGCTCACCCCTGTCCGGTCCTGTCCTGTCCTGTCCTGCCAG
Seq C2 exon
GGCCTGGCCGAGTACTGCACACTGATCGACAGCTCGTCCTCCTTCCGAGCCTACCGGGCCGCCCTCTCGGAGGTGGAACCGCCGTGCATCCCGTACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107263-RAPGEF1:NM_005312:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=FE(18.5=100)
A:
NA
C2:
PF0061714=RasGEF=FE(18.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAAGCTGAATAACTTCAACTCCT
R:
AGGTACGGGATGCACGGC
Band lengths:
194-1802
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)