GgaINT1023359 @ galGal4
Intron Retention
Gene
ENSGALG00000006348 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chrLGE22C19W28_E50C23:434647-435389:+
Coord C1 exon
chrLGE22C19W28_E50C23:434647-434793
Coord A exon
chrLGE22C19W28_E50C23:434794-435279
Coord C2 exon
chrLGE22C19W28_E50C23:435280-435389
Length
486 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGC
5' ss Score
7.93
3' ss Seq
AGGCTGCTTTTCCCATTTAGGAC
3' ss Score
9.3
Exon sequences
Seq C1 exon
GGCTTGGTGGCCACATTGCATGAAGGGGACGACTTTGGGCAGCTGGCACTGGTGAACGATGCTCCCCGAGCAGCCAGCATCATCCTGAGGGAGGACAACTGCCACTTCCTGCGGGTGGACAAGCAGGACTTCAACCGCATCCTCAAG
Seq A exon
GTGGGCAGCTGGGGGGGCTCCTGAGCTGGGCACCATCCCAGGACTCTCCTGGGGCTGTGGGGTGTGGGGTTTGCTCTGGGATGTGCAGAGTGTGGTGGTTGCAGGGGGATGGTTATCATTTGCAGTGAGCTGCCGTGCAGTGCCAGCAGGGTGCTGGGGTGCACTGAGCTGCAATGCAATGCCAGCAGGGTGCTGAGGTGCAGTGAACCACCATGCAATGCCAGCAGGGTGCTGGGGTGCAATGAACCACCATGCAATTCCAGCAGGGTGCTGGGGTGCAGTGAACTACCATGCAATGCCAACAGGGTGCTGGGGTGCACTGAGCTGCCATGTAATGCCAATGGAGTGCTAGGGTGCAAACAGCTGTGTGTGCAATGCACTTTGCAGCCCGTGCTGCTTGCTGCTGGCCGTCTTTGCCCAGGGACCGGCCTGGGGAGGACAGGCTGCAGCCACCAAGCCAGGCTGAAGGCTGCTTTTCCCATTTAG
Seq C2 exon
GACGTGGAAGCCAACACCATGCGCCTGAAGGAGCACGGGAAGGTGGTGTTGGTGCTGCAGAAGAACCTGCAGGGAGGCAGCAGCCAGCCGGCCGCCACGCGGAGCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006348:ENSGALT00000010260:9
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:
PF0002724=cNMP_binding=FE(55.8=100)
A:
NA
C2:
PF0002724=cNMP_binding=PD(2.3=5.4)
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:
TTGGTGGCCACATTGCATGAA
R:
GCCTCCCTGCAGGTTCTTCT
Band lengths:
222-708
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]