BtaINT0122396 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020984 | RAPGEF4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:HGNC Symbol;Acc:HGNC:16626]
Coordinates
chr2:23736658-23738462:-
Coord C1 exon
chr2:23738341-23738462
Coord A exon
chr2:23736842-23738340
Coord C2 exon
chr2:23736658-23736841
Length
1499 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
TGCCCCCATGTTTCCCGTAGTGG
3' ss Score
7.85
Exon sequences
Seq C1 exon
ACAGTGCTGTGTGGGGACCGAGCTGGTGGACTGGATGCTGCAGCAGACTCCATGTGTTCACTCCCGAACGCAAGCTGTGGGCATGTGGCAAGTCCTGGTAGAAGACAGCGTTCTCAACCATG
Seq A exon
GTAAGATGACACGCGGTCCCTGGAAAGCCCTCAAGAAATGCCAAGCGTGTTTCCCTGGGTTGGTTGTGGCTGAACTCCCACACGGGCCAGAAAGAATTATGATCTCTTTAGGGACCCGCAGAGCTGGCGTCTTCATTTAGCAATACAAATGCAGCAAATGGATGCCGTTGATTGCAGTGTTCCACCACTGTACCTTCCTAACTTGGGAGAACGTATGAAGGGAAAATGAAATTGCAACCCGAGTGCATTAGTTCCAATTATGTTTATTAGTTTGCATTCATGGTTCATTGATAGCGTGATTATACTCTGAGCATCGCACAGCAATCCTGATGCAGCGGCCAAATGAGAGCAATGAAGTGTGTGGCCAGGCTGATGACATGAAAGAGTAATGAATTCAGAACCTGCGTTTTCTGGGAGAGCCAATTTGTGTACCCACGCAATGACCGTATGTAAAATCATGCGTGCTCTATGGTTGTAGCCCCTGATATCTAAGCAGAGTAACAATTCAGGACAGGAGTGGGACTGTGGTTTAACTCTTCATGCCATTTGTTTAAGGATCACTTTTCCAAACAGACAAACTACTAAAATCTTTCCCTTAATACCTGGGAATGTAATGATGGTCTTGCCAGTGTTTCACAGACTTTACTGTGTATCCAGAACACCTGGAACTCTTGTTAAAATGCAGACTCTGATTCAGAGAGTCTGCATTTCCAACAAGCTCCCAGATGATGCTGATTCATATTTTTGAGCAGCAAGGATTTATCACTCCTTATCTTTGGACGGTGTTGATGCTCCCTCCTGAAAAGGAGCTTAAAACTTTAAGACACATAGATGACAGATTATAAACCAAGTTCATGACTTTGTCTTTCAGAGATCTAAATCTTCTGGTTTAAAGGCAATATGATTAAAAAAAAAAACTCTTTAAAACTTGAACTAGAAGGAAATTATTATTAGATACTAGGGGTATATGACCTAGATGGTTGGTCTTGTCAGCTTTGCTCAGACAATTTTATTTTAATTTTTAAAGTGCAGACAGACATGGTTATAAACAGTAGATATAAAAAGAAAAAAAATCAATTCTGATGCTGATAAAGTCAGGTTTTTTTCAGTCTGTACTTTGACAAAACCACTATAGAGCATGATCTGGCAGTTGGTCATTTTCCTCTTTGGGATGTGTAACCCACACACTAGAAAATGTCATCAAGGCAATTTCACTGGTCAGAGGGCTCATCTCAGGGAAGTTGGCCGGTTCTCATAGGAGAGTCCTAGGGCAGCTCAGGAGATGGGCGGGTCAGAGAGAGCTGTGAGGTGCACGCCTGCAACCCGGAGGTCCCGTCTTCCAGCTGCAGGGCCCTGGGCGAGGCCACGGGAAAAGGGTGAGGAGTCCCACCGCCTCGCTGCCACTTGGCTGTCTTGCCCGACACCATCATTCGTTTCTGGCAAACGGGCTGTGAGGCAGAGGTGCCCACGGCTGATGCTTGCCCCCATGTTTCCCGTAG
Seq C2 exon
TGGATCAGGAGCATCACTTCCAAGACAAATATTTATTTTATCGGTTTCTGGATGATGAGCATGAGGACGCCCCTTTGCCTACGGAGGAGGAAAAAAAGGAGTGTGATGAGGAGCTGCAGGACACCATGCTGCTGCTGTCGCAGATGGGCCCGGACGCCCACATGAGGATGGTCCTTCGCAAACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020984:ENSBTAT00000061074:9
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=0.274
Domain overlap (PFAM):
C1:
PF0061016=DEP=FE(57.7=100)
A:
NA
C2:
PF0061016=DEP=PD(21.1=24.2)
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:
ACAGTGCTGTGTGGGGAC
R:
GGTTTGCGAAGGACCATCC
Band lengths:
306-1805
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]