DreINT0124540 @ danRer10
Intron Retention
Gene
ENSDARG00000079291 | rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:ZFIN;Acc:ZDB-GENE-090312-38]
Coordinates
chr23:33502526-33502891:+
Coord C1 exon
chr23:33502526-33502604
Coord A exon
chr23:33502605-33502753
Coord C2 exon
chr23:33502754-33502891
Length
149 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGT
5' ss Score
7.81
3' ss Seq
AAGAGTTTGTTTTTTCTCAGTGT
3' ss Score
5.08
Exon sequences
Seq C1 exon
CTGAACCAAAAGTTTGATTGGTTTTCAGCTTACGAAGAGCCGGTGGGAAAACTGAGGTCGATTAAAGCCCAAGATAAAG
Seq A exon
GTTTGTGTTTTTACTTCTGTAAGATTTTATACCAATCCATAACACAAAGACATTAAAGAAAGTCCAGATAAACCTGTGAAATTGTTTTGATTAATCAAAATAGACTGGCTGGGATTTACCTTAATTAAGAAGAGTTTGTTTTTTCTCAG
Seq C2 exon
TGTTGTATGAGATCTTTAAACCGGATCATAAGGCTGTCACTGTGATGCTGCCAGTTGATGCATCGGTGAACGACATCTTGACTACATTAGTGGATCCTGACAGAAACTATGTGCTTGTCAAGATGAATTCCTCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079291:ENSDART00000142328:14
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:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAAAAGTTTGATTGGTTTTCAGCT
R:
TCCTGAGGAATTCATCTTGACAAGC
Band lengths:
211-360
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]