BtaINT0122342 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006828 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr5:32706564-32707049:+
Coord C1 exon
chr5:32706564-32706676
Coord A exon
chr5:32706677-32706960
Coord C2 exon
chr5:32706961-32707049
Length
284 bp
Sequences
Splice sites
5' ss Seq
TCGGTAACA
5' ss Score
5.35
3' ss Seq
GGACCGGCTGTTTCTTCCAGGTA
3' ss Score
7.73
Exon sequences
Seq C1 exon
GATGTGGAAGCAAAGACCATGAGGCTGGAAGAACATGGCAAAGTGGTGTTAGTGCTGGAGAGAACCTCTCAGGGCACTGGCCCTTCTCGTCCCCCAACCCCAGGCAGGAATCG
Seq A exon
GTAACACACCCGCCGTGTTCCCCTCTCCATACCATCTCTCTTGCCCACCTTCTCTTCTGTTTCCTGGGCTTTACTCCCTTCTCTGTGTCATATACCTGCCCGCTGCGGGTGGAGAGGCTTCCAGGGGTTAAGATGCATCCCCCGAGTTAGTCCCCCTTCCACCACACGGGGTGGGGAGAGGGCTGGCAAATAGGGGTGAGCGATATGATTGATTCTTGATGTCTGCCCCCGCTGCGGGAGCGGGAGTCGGGGCTCAAGTGCTATGGACCGGCTGTTTCTTCCAG
Seq C2 exon
GTATACAGTGATGTCTGGCACCCCAGAGAAGATCCTAGAACTTCTGTTGGAGGCCATGCGGCCTGACTCCAGTGCTCATGACCCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006828:ENSBTAT00000008976:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.194
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(2.4=5.3)
A:
NA
C2:
PF0061815=RasGEF_N=PU(25.5=90.3)
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:
TGGAAGCAAAGACCATGAGGC
R:
GTTGGGTCATGAGCACTGGAG
Band lengths:
196-480
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]