BtaINT0122349 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006828 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr5:32711786-32713851:+
Coord C1 exon
chr5:32711786-32711932
Coord A exon
chr5:32711933-32713753
Coord C2 exon
chr5:32713754-32713851
Length
1821 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
CAGCTCTGCTCTCTTTGCAGATG
3' ss Score
10.61
Exon sequences
Seq C1 exon
TCCCCTATGACATCTGCCGGCCAGACCACTCCATGCTAACCCTGCAGCTGCCTGTGACGGCCTCAGTGAGAGAGGTGATGGCAGCGTTGGCTCAGGAGGACGGCTGGACTAAGGGGCAGGTGCTGGTGAAGGTCAACTCGGCAGGTG
Seq A exon
GTGAGTTGTGTCTCTGGGTAGGGTGGCCCCAAGGGAGGGGGGCCCCCTCAGAGCTGTACCCACCCCCTGAATTAAGATCATCACCATCTTTGTCAGTGTTAATGGTAGTTAGCATTTATGGGAGGCTTATCACATCTTACTTATACATGTTACGTATAAGTCATGGACGACTCTTTGTGACCCCATCGACTGTAGCCCACCAGGCTCCTCTGTCCATGGGATTTCCCAGGCAAGAATACTGGAGTGGGTTGCTATTTCCTGTTCCAGGTGATGGGCACAGACCCAGGGATTGAACCTGCGTCTCCTGCTTGGCAGGTGGATTCTTTACCACTGAGCCACCAGGGATGCCTGACATTATTACCATGCTTACATATTTATTTAATCCTAATAGCAATCTTATGAGATAGGTACTTTTATCCTATTTTCAGACAAGGAAACTGAAGCTCAAATGGATTCAGTGATTTTTTCCCCAGGCTTCCCCTTTGAGTGCATAGACAGACTTTGAATTTAGGTAGTTGCTCATTTAGTCCATCAACATCTTTGAGGGTCACCTATGGGCCAGCAGCATTTAGGAGGCAGACTTACCATGGCAGGTAAGATGAGCAGCTTGATGGTTAAGAGCCTAGACTGTGGACACCCAGACCCGAGTTGCAATCCCAGACCCACGGCTTACTGACTGTATGATCCTGCCCAAGTTGTTTGACCTCTGTGAGCTTGCATTTCCTTGTCTGTTGGATGACCACTGTAACTACCTATCACTTAGGATTGCTATGGCTATTAAATGAGCTACTGTGTTTGAAGCTCTTAGCATGGGACCTGGCATAAAGTTGGTGCTCAGAGTATGGCAGAATGAGGATTATTAAGACCTGCCTTTAGAGAACTTGGGACATTAAAAACCACTGTTATTCATGAAAGACACAGAGCATGGGTATGACAGCGGAGTGGGAGCCCAGGGTAAGCCGCTGGTCATCCAGAGAATAATGGCAAGGGGTGGCAGGGAGACCAGCAAAGCCTCCTTCGTTCAGGAAGGAGAGATACTGAGAGCACCAGGGCCTGTGTGCTCCTCTGGGAAGCACTGCCCTCTGGTGGCCATGTGGCAAGTTGCAGTTGTCCAAACCCAGTGTTTAGAGCACTGATTGTTTTGATGGACACCCATGACAGTAATCAGTATTTTATTACAGACTCCCTTATTTGTGTATATTTCCTTGCAAGTCACATACATACATTCCTACACTGTTGCTATGTGATCATAGAGCAACACACAAAGCAAATACAAAACAGGTAAGAAAAATCAGTATAAGTGCTAATATTTTTTTCCTGGACGCATGGAATGGTCTTGTGTACCTTACTTTGAAGACTACTGGTCTAGGGACTGAGGGCTCAAGCATGACTGAAAACCCAGTCCCAGTCCACAAGAGCTGATGGAAATCCACACGAAGATTTCTGTAAGGCATTTCCCAATTTTCAAAGGGCTTGTATATGTATCATATCCTTATAGCCGCTATTTATATCAATGACTTCATTTGACTGATGAGTAGTCACGGGAAATCTTGGTGTCTGCTTTTGACAAAGGAGGAAGCTGGGACTCAGGGAGGCTCCAGCGTCGCCCAGTGTCAGCCTGTCTCCCCAAGACTCCTCTTTCATTGTCCTCTGGCCATGTTGCCCCTGTGCATGTGTGGGCATGCGCACCCATGCATTTAGAACACCTGCCTAGACTCCAGTGCTGCTATTGGGAGACCTCTTCCAGCCTCCACCCCGCCTCCGGTTGCTCCCTGGCCTCCCTCTCTGTCCCCACCCAGCACAGCTCTGCTCTCTTTGCAG
Seq C2 exon
ATGCCATTGGCCTGCAGCCAGATGCCCGTGGTGTGGCCACATCCCTGGGGCTTAACGAGCGGCTCTTTGTTGTCAACCCACAGGAAGTGCACGAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006828:ENSBTAT00000008976:18
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=0.091
Domain overlap (PFAM):
C1:
NO
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:
TCCCCTATGACATCTGCCGG
R:
GTGCACTTCCTGTGGGTTGAC
Band lengths:
239-2060
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]