DreINT0017702 @ danRer10
Intron Retention
Gene
ENSDARG00000075924 | RAPGEF4 (1 of 2)
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:HGNC Symbol;Acc:HGNC:16626]
Coordinates
chr6:6748662-6749031:+
Coord C1 exon
chr6:6748662-6748768
Coord A exon
chr6:6748769-6748945
Coord C2 exon
chr6:6748946-6749031
Length
177 bp
Sequences
Splice sites
5' ss Seq
CAAGTATGT
5' ss Score
7.44
3' ss Seq
GTGTGTGTTGTGTTGTATAGATA
3' ss Score
7.72
Exon sequences
Seq C1 exon
GATGTTGAAGCAAACACGGTGCGTCTAAAAGAGCATGAGCAGGATGTTTTGGTACTACAGAAGAGTCTCCGGCCCTCCAGCCATGGAAACATCCCAGCCCACTTCAA
Seq A exon
GTATGTCTTTTCAGTTTATCTGCACCGTTTTGACCCATGGACAACAAACAAATCCAGTCATTCAGTTATTTATTCAAACCTCTATGTGTGTGTGTGCGTGTGTGCGTGTGTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTGTGTTGTATAG
Seq C2 exon
ATACACTGTGATGTCAGGCAGCCCTGAGAAGATTCTGGAGCATCTGCTGGAGACAATGCGACTGGACATTCATTTCTCTGACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075924:ENSDART00000166607:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(2.3=5.6)
A:
NA
C2:
PF0061815=RasGEF_N=PU(24.8=90.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGCAAACACGGTGCGTCTAA
R:
CTGGGTCAGAGAAATGAATGTCCA
Band lengths:
186-363
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]