BtaINT0122350 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006828 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr5:32713754-32714354:+
Coord C1 exon
chr5:32713754-32713851
Coord A exon
chr5:32713852-32714228
Coord C2 exon
chr5:32714229-32714354
Length
377 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGG
5' ss Score
6.35
3' ss Seq
GAGCACTCTTCCACCTGCAGACC
3' ss Score
8.46
Exon sequences
Seq C1 exon
ATGCCATTGGCCTGCAGCCAGATGCCCGTGGTGTGGCCACATCCCTGGGGCTTAACGAGCGGCTCTTTGTTGTCAACCCACAGGAAGTGCACGAGCTG
Seq A exon
GTAGGGCCAGGCAGGGCGCCAGGGCCCCGGGAAGGGCTGTTTTGGGAGTGGTACGGGTGGGTGCTAGGAGACAGCCACATGGAAAGGAGAGCAGGGCCTGGCTGTGGCTGCTCCTAAGGAGGAAGAGAGAGGAGTGGGCCTCAGCCGATGGAGGAAGTCCCAAGGGGAAAACTGTTGGGAGCTCTCAAGTGGGAGGGGCCCAGCACTGGGGAGCTGTCAGGGCATGCTTCCTTGGGGCATGCCTCCACTTCCTGCAGCACCTCTGCCCTCCTGACGTGCCTCCGGCCCTGGGCACAGACTTTTGGCCCCAGACTCTCTCCCCCAACCATGCCCCCTGGACTCCCCAGGCACCCCTCTGAGCACTCTTCCACCTGCAG
Seq C2 exon
ACCCCACACCCCGATCAGCTGGGGCCCACTGTGGGCTCTGCCGAGGGGCTGGACCTGGTGAGCACCAAGGACCTGGCGGGCCAGCTCACGGACCACGACTGGAGCCTCTTCAACAGCATCCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006828:ENSBTAT00000008976:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.091 A=NA C2=0.262
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061714=RasGEF=PU(12.9=57.1)
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:
CCAGATGCCCGTGGTGTG
R:
TGGTGGATGCTGTTGAAGAGG
Band lengths:
206-583
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]