GgaINT1023358 @ galGal4
Intron Retention
Gene
ENSGALG00000006348 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chrLGE22C19W28_E50C23:434444-434793:+
Coord C1 exon
chrLGE22C19W28_E50C23:434444-434520
Coord A exon
chrLGE22C19W28_E50C23:434521-434646
Coord C2 exon
chrLGE22C19W28_E50C23:434647-434793
Length
126 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TAAGCCCTGTCCCCTTGCAGGGC
3' ss Score
9.93
Exon sequences
Seq C1 exon
TGTTCAGCCAAGGGGATAAAGGCACCTCGTGGTACATCGTCTGGAAGGGTTCGGTGAATGTGGTCACCCACGGCAAG
Seq A exon
GTAGGTGCGTCCCCACGCAGCCACCCCATCCTTGCTGCCACCTCGGTGCCAACGGGCACCCCATTTCTCCAACCTGGCGTGGGTCAGGTCCGGCTTTGGGTTTGGGTAAGCCCTGTCCCCTTGCAG
Seq C2 exon
GGCTTGGTGGCCACATTGCATGAAGGGGACGACTTTGGGCAGCTGGCACTGGTGAACGATGCTCCCCGAGCAGCCAGCATCATCCTGAGGGAGGACAACTGCCACTTCCTGCGGGTGGACAAGCAGGACTTCAACCGCATCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006348:ENSGALT00000010260:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=FE(29.1=100)
A:
NA
C2:
PF0002724=cNMP_binding=FE(55.8=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:
TCAGCCAAGGGGATAAAGGCA
R:
GAGGATGCGGTTGAAGTCCTG
Band lengths:
218-344
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]