BtaINT0122340 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006828 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr5:32697065-32698027:+
Coord C1 exon
chr5:32697065-32697338
Coord A exon
chr5:32697339-32697814
Coord C2 exon
chr5:32697815-32698027
Length
476 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
CCGTCCTCTTCCCATCACAGGTG
3' ss Score
10.54
Exon sequences
Seq C1 exon
GAGGCTCGGGGTTCCTTGTCGCTGGGGGCTGGGGTGACGTTGTCCCCCCACCAAGTCCCCAGTTCTCCCCCAACCCGAGAGGAGCCTTTCCACCCAGCCTGGCTGGGGCTGCCTTGGAAGCGGCTCCAGCTACGAATTGGTCGGCTCACTTCTCCTGGGACTTACAGGCCGGGGGCACACAGTGGCTCGTTGTGGGGCGGGCGGGTGCTCCCGCCACCCCTTGCCTTCTGCTAGAGCCTGCAGGGCTGTGCGAGCTTGAAGGAGGAACATGAAG
Seq A exon
GTGGGTATGATGGGGTGGGGGCAGGGGAGGAGGAGCAGAGGAGGAAGCTGACACGGTGGGGGAGTTGGGGTGGGAGACAGAGGCTTGGTCAAGGGTGAGGAGGGAGGAGAAAAGAAGGGTTTGAGCTGAAGCTGCGTTTCTCGGGGATCCAGTGAGTCCGCAGCTCCATTCTGGGAGTTGGTGGAGATCCCTGCAGGTCCATGGTCGGTGGGGTGGGGCAGAATTCCAAAGAAGGGCCTGATCTCTGGTACGCCGCCGCCGCCGCCGGCTGGAGACCCCTAAGTGCGCCAGACCGGCAGGCCCCAGTGAAGGTCTTCCTGTCCCTCCCCCGGCTCCTGGCAGGGGCGCAGCACCTCCGCCTGACCAGTACAGAGGATTCGAAGGAGGTGCTTCTGCTTGGGGCAGCCGAGCCGTGCTTTGGTCCAGCTGCCCCGGACCCAGCCTCATGGCTGTCTGCCGTCCTCTTCCCATCACAG
Seq C2 exon
GTGGGCTGGCCAGGTGAGGGCCGCTGGCAGGTGGGCCTGGCTGTAGAGGGCGACTCGATTCTGGGAGCACCGCCGTTGGGAGGCCTCCCGGACGTGGTGCCGGAGGGGACGCTGCTCAACATGGTGCTCAGGAGGATGTATCGGTCCCGAAGCTGCTCCTACCAGCTGCTGCTCGAACACCAGCGCCCCAGCTGCATCCAGGGGCTGCGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006828:ENSBTAT00000008976:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 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
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCAAGTCCCCAGTTCTCCC
R:
CCTGAGCACCATGTTGAGCAG
Band lengths:
357-833
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]