GgaINT0124549 @ galGal3
Intron Retention
Gene
ENSGALG00000003712 | RAPGEF1
Description
NA
Coordinates
chr17:6874561-6874950:-
Coord C1 exon
chr17:6874866-6874950
Coord A exon
chr17:6874656-6874865
Coord C2 exon
chr17:6874561-6874655
Length
210 bp
Sequences
Splice sites
5' ss Seq
GAGGTACGG
5' ss Score
9.4
3' ss Seq
CTGTTTTTCTTCCTGGGCAGATA
3' ss Score
11.04
Exon sequences
Seq C1 exon
GCCGGGCACCTTGCATGATTTCCACAGTCATGAAATAGCCGAGCAGCTGACACTCTTAGATGCTGAACTCTTCTATAAAATCGAG
Seq A exon
GTACGGAGACGAGGGCAGGGGGAGGGCAGAGGGAGGAGGGGTCTGCACACATCCCCTCTGCGATCCCTGCTATTCCCAGCACACCGCAGGAGAAGCTGAACTTGTGTCAGCAAAAGACCACGAGCACAGGCTGTGGCTGGGAATCTTAAGGCAGAGATCCCATGATAACGTGTGGTATTCTCCCACCCCTCTGTTTTTCTTCCTGGGCAG
Seq C2 exon
ATACCAGAAGTTTTGCTTTGGGCGAAAGAGCAAAATGAAGAGAAGAGCCCCAACCTGACGCAGTTCACAGAGCACTTTAATAACATGTCCTACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003712:ENSGALT00000005891:20
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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACCTTGCATGATTTCCACA
R:
TAGGACATGTTATTAAAGTGCTCTGT
Band lengths:
172-382
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]