BtaINT0122358 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006828 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr5:32717008-32717227:+
Coord C1 exon
chr5:32717008-32717062
Coord A exon
chr5:32717063-32717155
Coord C2 exon
chr5:32717156-32717227
Length
93 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
ACTCTCCCCTCACCCCCCAGTGC
3' ss Score
10.26
Exon sequences
Seq C1 exon
AGAATGATGGCCAGAGCTGCACGGATGCTACACCACTGCCGAAGCCACAGCAATG
Seq A exon
GTGAGAGGGCAGATCCCCGGTGGGCGCCCCTGAGTGATGTCCCCTTCAAGGCACCAACTTGGTCTCCTCACTGACTCTCCCCTCACCCCCCAG
Seq C2 exon
TGCCTCTGTCACCGCTCAGAAGCCGAGTCTCCCACCTGCACGAGGACAGCCAGGCGGTCAGGGTTTCCACGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006828:ENSBTAT00000008976:26
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=0.160
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PD(0.5=5.3)
A:
NA
C2:
NO
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:
AGAATGATGGCCAGAGCTGCA
R:
ACGTGGAAACCCTGACCGC
Band lengths:
127-220
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]