BtaINT0122371 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020984 | RAPGEF4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:HGNC Symbol;Acc:HGNC:16626]
Coordinates
chr2:23710727-23711368:-
Coord C1 exon
chr2:23711292-23711368
Coord A exon
chr2:23710874-23711291
Coord C2 exon
chr2:23710727-23710873
Length
418 bp
Sequences
Splice sites
5' ss Seq
AAGGTATAT
5' ss Score
7.84
3' ss Seq
GCATGATTTGTTCTCTCCAGGGT
3' ss Score
8.1
Exon sequences
Seq C1 exon
TATTTAACCAAGGGGAAGAAGGCACCTCCTGGTACATTATTCTAAAAGGATCAGTGAATGTAGTCATTTATGGCAAG
Seq A exon
GTATATATTTTTTTTCTTTTGAAACTTTATTATGCTGCCTTTACTACTGGCTCTAAGTATTAAGAATGTAATGCTACAGTTAAACTTGCTACAATATTGGTACTCAATGTAGAAAAGACATTATAGCCTCTCTAATCATATACTATCTAAATTTTTATACTCAGAGTAGCACTGAACTTTCTGGGACTCATGGATTATAATGTATGTATGTAAGTTAGGTCCTAGCACACGTTACTCAATGAAAGAAAAATGAAACACTATAATTTAATTTTGTGATCCCCTCCCCCGTGACTTCTCTGGGTACAGCCTGTTGATATATATTCAGTGTTTTCGGGGCAGAGGGGCTTGTGGTGTGAGGCGGGTGGGTGTGTGCCCTGTTCCAGGGATCACCTTCATCTGCATGATTTGTTCTCTCCAG
Seq C2 exon
GGTGTGGTCTGTACCCTGCATGAGGGCGATGACTTTGGCAAGTTAGCCCTAGTGAATGATGCCCCAAGAGCTGCCTCCATCGTCTTGAGAGAAGATAACTGCCATTTCTTAAGAGTAGACAAGGAGGATTTCAACCGGATCCTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020984:ENSBTAT00000061074:13
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=0.000
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=FE(28.7=100)
A:
NA
C2:
PF0002724=cNMP_binding=FE(55.2=100)
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:
TTTAACCAAGGGGAAGAAGGCAC
R:
CCTCAGGATCCGGTTGAAATCC
Band lengths:
222-640
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]