BtaINT0122348 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006828 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr5:32711421-32711932:+
Coord C1 exon
chr5:32711421-32711502
Coord A exon
chr5:32711503-32711785
Coord C2 exon
chr5:32711786-32711932
Length
283 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGT
5' ss Score
8.46
3' ss Seq
AGTCCCATCTTCTTCTCCAGTCC
3' ss Score
7.45
Exon sequences
Seq C1 exon
GCCCGGAATGTTCCCGTTTGGCTCCCCAGCCAGGACGAGCCTCTCCCTAGCAGCAACTGTGCCATCAGAGTTGGGGACAAAG
Seq A exon
GTTGGTGGTCTGAGTCCGCCAGGGCAGAGCTCAAACCCTGCTCTCTCACCACCCTTGACTTTGGGGTGCCTGGCCCAGAATGGCATGTTGTGCTCCTTGGGGTCTCTGTTTCAGGCTCCCCCCTTGCTCACCTCAGGGTCTCCCACCTGCCTGCCCAGGCTTCTCCTTAGTGCTGTTGCCCCCAGTCCTTGGGACCCTCCCTTGCTGCAGTCACTGCCTTCTCCCTGCTGGGGTGGGGAGACCAGGCGGCTCCCTCCCAATTCAGTCCCATCTTCTTCTCCAG
Seq C2 exon
TCCCCTATGACATCTGCCGGCCAGACCACTCCATGCTAACCCTGCAGCTGCCTGTGACGGCCTCAGTGAGAGAGGTGATGGCAGCGTTGGCTCAGGAGGACGGCTGGACTAAGGGGCAGGTGCTGGTGAAGGTCAACTCGGCAGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006828:ENSBTAT00000008976:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.250 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCGGAATGTTCCCGTTTGG
R:
CACCTGCCGAGTTGACCTTC
Band lengths:
228-511
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]