BtaINT0122341 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006828 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr5:32705888-32706676:+
Coord C1 exon
chr5:32705888-32706034
Coord A exon
chr5:32706035-32706563
Coord C2 exon
chr5:32706564-32706676
Length
529 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCCG
5' ss Score
5.74
3' ss Seq
GGGTGTGGCTTGTTCTCCAGGAT
3' ss Score
7.35
Exon sequences
Seq C1 exon
GGCCTGGTGACCACCCTGCACGAGGGAGATGACTTCGGACAGCTGGCTCTGGTGAACGATGCACCTCGGGCCGCCACCATCATCCTGGGAGAAGACAACTGTCATTTTCTTCGTGTGGACAAGCAGGACTTCAACCGTATCATCAAG
Seq A exon
GTGCCGCTGCTGGGGGTGGGGAGGGCAGGGACATGTGTCTGGAGAAGTGGTGTGGGGCAAGGAGTAGGGACCAGATGGACACTTTAAGGAGTAGGGAGAGGTCAGAGGTGGAAACCTTGGGGATGATGGCTGGAGGAGGGAGCCCAGCTCTGGGTGTGTGAGGAGGTGCGTGGCTTGCTGAGGAGGCTCAGTGAGCCCTGGGAACCCTGGTTCCCGTGGGAGACCAGGGGTGAGGTTACAGAGGGGTGAGGGTCTGGGGTGCAGGGGGAGGCGGCGTAATGGAGAGTGGGGTCCATAGAAGGAGCCCTGGGAGGGACAGGGTGGAGGAGGGGCTCAGGCTGGGTGAGAGGCACCAGTGAGGGACAAATCTAAGGTTGTGGGCGTTGACTAGGGCGGGAGAAGGGCTGTGGGTCCTTGTGGGAGCCTTGTGGGGCTTGGAGTTTGGAATGGGGGAGGCAGAGGGAGAGGCCCTAGAATGGGTAAAGGAGTTGTGGTGTGTTTTGAGCACTGGGTGTGGCTTGTTCTCCAG
Seq C2 exon
GATGTGGAAGCAAAGACCATGAGGCTGGAAGAACATGGCAAAGTGGTGTTAGTGCTGGAGAGAACCTCTCAGGGCACTGGCCCTTCTCGTCCCCCAACCCCAGGCAGGAATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006828:ENSBTAT00000008976:10
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=0.500
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=FE(56.5=100)
A:
NA
C2:
PF0002724=cNMP_binding=PD(2.4=5.3)
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:
GTGACCACCCTGCACGAG
R:
CGATTCCTGCCTGGGGTTG
Band lengths:
254-783
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]