DreINT0124555 @ danRer10
Intron Retention
Gene
ENSDARG00000079291 | rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:ZFIN;Acc:ZDB-GENE-090312-38]
Coordinates
chr23:33493390-33494159:+
Coord C1 exon
chr23:33493390-33493466
Coord A exon
chr23:33493467-33494012
Coord C2 exon
chr23:33494013-33494159
Length
546 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
GTAAAGATGATCTCATTCAGGGC
3' ss Score
1.94
Exon sequences
Seq C1 exon
TGTTCAGTCAGGGGGACAAAGGGACTTCCTGGTACATCATCTGGAGAGGCTCTGTTAATGTCATCACACACGGCAAG
Seq A exon
GTAAAGCCATTTACCTTCAGCTGAGTGACTTTGAGTTTAAATTTAGATAACTTGCATTGTTTGAAGGTAATTCATAATGTGTGTTTTCTATAAAGATAAGATCATCTTGTGTATGTGCATGATAAATGACTCTAAAAAGGTGTTAAACATATCAGTGAGCATATGTTTATAAAACTTTGCACTTTCCTGTACAATTAAATTAAAATGATTTAATCTCAACACATCTCACACATATTATTTTTTTATTGTTTTGATTATTATTATTTAAAGTTTGTGATGTTTGTAAGTCACTTTGACCTGCATACTTTAATTAAGGCAACTGTACTGACACAAAAATATAAAATATTATTAGCACAACAATAATAACTATACTATTAAGCTAAAATATAACTGCTAACTTTATTTTGTCATACACAGATAGTTAAAAATAAGCAATCATTTTATTTGTTTTGTCTATCTGAATCACTATTGAATTTAAATACAAATACTTCCATTGTTGGACTATAAAGTGTGTGCTGCATCTTAAGTAAAGATGATCTCATTCAG
Seq C2 exon
GGCTTGGTGACTACGCTTCATGAAGGAGATGATTTTGGCCAGTTGGCATTGGTGAATGACGCTCCTCGAGCCGCCACCATCATTTTAAGAGAGGACAATTGCCACTTTCTGCGGGTGGACAAGCAGGATTTTATACGCATTCTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079291:ENSDART00000142328:6
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
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCAGGGGGACAAAGGGACTT
R:
AGAATGCGTATAAAATCCTGCTTGT
Band lengths:
214-760
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]