DreINT0124591 @ danRer10
Intron Retention
Gene
ENSDARG00000075271 | rapgef5a
Description
Rap guanine nucleotide exchange factor (GEF) 5a [Source:ZFIN;Acc:ZDB-GENE-030131-7681]
Coordinates
chr19:2856244-2856493:+
Coord C1 exon
chr19:2856244-2856294
Coord A exon
chr19:2856295-2856405
Coord C2 exon
chr19:2856406-2856493
Length
111 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
CTGACTGTTCTCTTCCTCAGGAT
3' ss Score
11.41
Exon sequences
Seq C1 exon
AAAGTTCCTGGAAAGTTCAAGAAGCTTTTCTCTGAGCTCGAGCTGTTGACA
Seq A exon
GTAAGTGATGTACAACACATACAGATAGGGCTCGTTTTGATTGCATCTCCACTTTTGTGCCGCTAGAGGTCAGTAATGTTAAGAGAATCGTCTGACTGTTCTCTTCCTCAG
Seq C2 exon
GATCCATCCATGAACCACAAAGCCTACAGAGACGCTTTCAAGAAAATGAAGCCGCCCAAAATACCCTTCATGCCGCTGCTGCTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075271:ENSDART00000112414:13
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=0.033
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=FE(8.6=100)
A:
NA
C2:
PF0061714=RasGEF=FE(15.7=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:
AAAGTTCCTGGAAAGTTCAAGAAGC
R:
GCAGCGGCATGAAGGGTATTT
Band lengths:
130-241
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]