BtaINT0122304 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020791 | RAPGEF1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:HGNC Symbol;Acc:HGNC:4568]
Coordinates
chr11:101732453-101732774:-
Coord C1 exon
chr11:101732690-101732774
Coord A exon
chr11:101732548-101732689
Coord C2 exon
chr11:101732453-101732547
Length
142 bp
Sequences
Splice sites
5' ss Seq
GAGGTACAG
5' ss Score
6.62
3' ss Seq
GGTCCCCCTGCTTTTTTCAGATT
3' ss Score
9.47
Exon sequences
Seq C1 exon
GCCCGGGACCTTGCACGACTTCCACAGCCATGAAATAGCCGAGCAGCTGACTCTGCTAGATGCCGAGCTCTTTTATAAAATAGAG
Seq A exon
GTACAGCCATGCGTGGGGCTGGCGGGGTGGGGGCTGTCCCTGGCCCGGGTGAGCACTGCTGCTCGTCCCCGAGTGAGAGGAGCTGCTGCTCCCAGCAGAGCCGGAGGGCCCGGGTTCTAGCTGGTCCCCCTGCTTTTTTCAG
Seq C2 exon
ATTCCTGAGGTTTTGCTTTGGGCTAAAGAGCAGAACGAGGAGAAGAGCCCGAACCTGACCCAGTTCACGGAGCACTTCAACAACATGTCCTACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020791:ENSBTAT00000032663:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.094
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(12.9=79.3)
A:
NA
C2:
PF0061714=RasGEF=FE(17.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGGGACCTTGCACGACTT
R:
CAGTAGGACATGTTGTTGAAGTGC
Band lengths:
178-320
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development