BtaINT0122359 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006828 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr5:32717156-32718624:+
Coord C1 exon
chr5:32717156-32717227
Coord A exon
chr5:32717228-32718201
Coord C2 exon
chr5:32718202-32718624
Length
974 bp
Sequences
Splice sites
5' ss Seq
CGTGTAAGT
5' ss Score
8.58
3' ss Seq
CCGCCCTCCCTGCCCCCCAGGCT
3' ss Score
9.06
Exon sequences
Seq C1 exon
TGCCTCTGTCACCGCTCAGAAGCCGAGTCTCCCACCTGCACGAGGACAGCCAGGCGGTCAGGGTTTCCACGT
Seq A exon
GTAAGTGAGGGCAGGGGTGGGTGCTGACAAGCTGGCCGCGGCTGGCTGGCACTTACAGGCACATCCATACATGAAAGGGCTTCCCCAGTGGCTCAGATGGAAGAGAATCTGCCTGCAATGAGGGAGACCTGGATTCAATCCCTGGGTTGGGAAGATCCAGTATTCTTGCCTGGAGAATCGCATGGGCAGAGGAGCCAGGCGGGCTACAGTCCATGGGGTTGCAAAGCACGATGTTGATAATGGTTCATAACAGCTGTATGAAGTAGGTAGAGTATTATCCCCACTTAAAGGTATACAGTGGGCTGGAAGCCTTGAAAAAACAGGTAGAAGCCGCAGTGAGGTAGAGCTGGTTAGATAAGCAGTTAGACAGGGCTGGGACCCACGCACTCCTACTCCAGGCCTGTGTTCTTTTAACTGGCCTTCAGTTTGTGAGAAATGGGATTAGTCGTAATCCACAGTTCGTACCACACCATCATCATTATCTTATGCATTTATCTATTCTGAAAATAAGATGAGCCCTTCTGGACCCAAGCCAAGCTTCAGCACACTGACAATAACTTCCATCTCCCTAGTGGTGGTCCCCTTTCCGGTCTCCTTGCCCCTCCCCACCCAGGGAAACCACTATGCTGAATTTTGAGTTACCCATTTCCTTGTTTTTAAAAAATAGCTTGATCGTGTGTACATATAATAAAATATACATATACATATATCTTTAAAATATCTCATATATATATGACAACAAAATATTCTTTAGTTTTCATTGTTTTTGAACTTGGTAAAAGGGGTATTAAGCTGCATATAATTTTGGGGCCTGTTTCACTGTGCTCTTCTGTCCCAGATGGGGGATGGGGTGTCTTCTAGATTGGCTGTGGGAAGTGGCAGGCTGGGTAGCACAAGGTAGGAGGATCGATTTGCCTCTTGGAAAGGGGAAAGGTGGGCTCTACAAAGTGCTGACCGCCCTCCCTGCCCCCCAG
Seq C2 exon
GCTCGGAGCAGTCCCTGAGCACCCGGAGTCCCGCCAGCACCTGGGCTTACGTCCAGCAGCTGAAGGTCATCGACAACCAGCGGGAACTGTCCCGCCTCTCCCGGGAGCTGGAGCCGTGAGGAGGGGCTGGGCTGGAGCAGACACTGGCCACCAGGAGAGCCTGGGGCACGCCGGGCGAGGAGGCCCACGGGCTGGCCGAGCCGGGCAGGGCTCTCCAAGGACTGGACCTGAGGCCCAGGAGAGGGCAGCGTGGAGGCACCTGTCCCCCGCGATGACTGGTGGCCAAGGAGGACCTGCGAATGGAAGGAGCTGGGGCCCAAGGCCAAGGAGTGGGGGACAGAGAGGCCCTGGAGTGAGTGGGAGAGCAGAGCGTTTTCTCTCTTTGTGTTCAATAGAGAGCTCTCCACACCAGGATTTTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006828:ENSBTAT00000008976:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.160 A=NA C2=0.231
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA

Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGAAGCCGAGTCTCCCA
R:
CTCCTTGGCCACCAGTCATC
Band lengths:
348-1322
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]