DreINT0017700 @ danRer10
Intron Retention
Gene
ENSDARG00000075924 | RAPGEF4 (1 of 2)
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:HGNC Symbol;Acc:HGNC:16626]
Coordinates
chr6:6746040-6746377:+
Coord C1 exon
chr6:6746040-6746116
Coord A exon
chr6:6746117-6746230
Coord C2 exon
chr6:6746231-6746377
Length
114 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
GTGTGTGTGTGTGTGTGTAGGGT
3' ss Score
9.19
Exon sequences
Seq C1 exon
TGTTTAATCAAGGGGAGGAAGGCACTTCTTGGTATATTATCCAGAAAGGATCAGTAAATGTTGTCATCTATGGCAAG
Seq A exon
GTAATGTCAGCTTTCATGTTTACTTACATTAATGTTAATGATTTCATAAATAGTGGCAAATATTAGATCAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAG
Seq C2 exon
GGTGTGGTTTGTACGCTGCATGAGGGAGATGATTTTGGCAAACTGGCGCTGGTAAATGACGCCCCCCGCGCCGCTTCCATCGTGCTGAGAGAGGACAACTGCCACTTCCTGAGGGTGGACAAAGAGGACTTCAACCGTATACTCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075924:ENSDART00000166607:12
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(62.5=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:
TAATCAAGGGGAGGAAGGCAC
R:
CCTGAGTATACGGTTGAAGTCCT
Band lengths:
220-334
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]