GgaINT0124552 @ galGal3
Intron Retention
Gene
ENSGALG00000003712 | RAPGEF1
Description
NA
Coordinates
chr17:6873296-6873895:-
Coord C1 exon
chr17:6873794-6873895
Coord A exon
chr17:6873394-6873793
Coord C2 exon
chr17:6873296-6873393
Length
400 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
GGGGCTTTGTGTTCTGCCAGGGC
3' ss Score
6.57
Exon sequences
Seq C1 exon
CACTTACGAAAGCTGAATAATTTTAATTCCTATCTGGCCATTCTTTCTGCACTGGATTCTGCACCCATCCGAAGGCTGGAGTGGCAGAAACAAACCTCAGAG
Seq A exon
GTGAGGAACAGTGCAGGCTTTCACATGTGGGGGGAAGAGGATAACTGTGGTTGCGATATGAAGCAGCAGGGTGAGTTTTAACAGCTCAGCAGCATGGCAGGGTGGAGGGATGGCGGATGAATGCTCTCCAGTGGGTGTAATGGCACAGTGCTGGCAGCCTGCAGTGCTGCGGGGCTTTCTGACAGCTGCAGAAGTGCCAGCACTGCCACGGGCTGAGGGGACAGCTGCTTCCTCCCTGTGCAGTGAAGCTCTGGTGGAGCTGAAGGCAGTGAAGTTCTGTGTGAACGCAGCAAGGCTCAGACTGAGCAAACGCACTGGTGGTGGTTGCAGGGTGGCATTGAGTCCCCTGGAGAGGGGTTACAGAGATAAAGGGGTGATTGGGGGCTTTGTGTTCTGCCAG
Seq C2 exon
GGCCTGGCTGAGTACTGCACACTGATCGACAGCTCCTCGTCCTTCCGCGCCTACCGTGCAGCCCTGGCTGATGTGGAGCCTCCCTGCATCCCATACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003712:ENSGALT00000005891:23
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=0.000
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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATTTTAATTCCTATCTGGCCATTCT
R:
AGGTATGGGATGCAGGGAGG
Band lengths:
182-582
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]