DreINT0124542 @ danRer10
Intron Retention
Gene
ENSDARG00000079291 | rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:ZFIN;Acc:ZDB-GENE-090312-38]
Coordinates
chr23:33504071-33505332:+
Coord C1 exon
chr23:33504071-33504168
Coord A exon
chr23:33504169-33505206
Coord C2 exon
chr23:33505207-33505332
Length
1038 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
GTGTGGTTTACCTCTGACAGACA
3' ss Score
5.56
Exon sequences
Seq C1 exon
ACAGAGTCCAGCTGAAGTTGGAGACCACAGCAGTGTCTGCCTCTTTAGGAGTGAACGAAAAGCTTTTCCTCTGCACTTCCAGCCAAGTTGAACAACTG
Seq A exon
GTGAGAGATGCCAACATGATTACCACCTTTATATAGTAAAAACACTCTAGAAATGAGCTGTAATATGCTTAACTCTGATAAATCTGTTGTTCTATGCATAAAAAACTGCATTAGAAATCAATTGATTAGGTAAGAGACTCGAGACTAAACAAGAGTCAGTTCAACTTTTGGTTCAGCTGAAAAAAGATGACTAAACTGGATATAAGTCTCATGATTTGAAGAAATTTCAATATAATTATTGTACCCAGATGTAAAAAAAAAATTACTTATTTATTATAAATTCTATAGAGTACAAAAGGAACATTTCTATTTTAACATTTTTTTCATACAATAACAATTAATGGCTACTAATAATTTAAACTTGAAAAAAAAAACTGCTAAAGTGATTTTTAACAATATGACGTTTAAAGATCCTTGTAACTAATTATTTTGCCATAATTATGCAATACCTTCAAACAATCTCAATATGTCAGCTTTTCTAAACAATAATTGGTTTGTTTTTATTGTATTTATTTAATCTGAGTAATCAATATCAATATATACACATGTAATTATGGAACCAGACAAAATGACAAATATTAGTCTGTATGCTTCTCTGTCAACTAGCATAGAAGAGTCTAAGTGCACCAGCAACCACTTAGAAACCATCCAGAACAAGACATCTCAACATCTTAAACGTCCTAGAAACCATCTATAGCACCTTAATTAAACCCAAGCAACTGCAAAACAATATTTCAGACAACAATCTGATTACCTGATCAACACAGACCTTAGAAATCTCACAGCAACCTTGAAGTCTCTAGAAAATCCGTAACAATATCCTAGCAATTGCCCAGAGTAATTTAGCAACCCCAGAGTAGCCACACAGAACACCTTAGCAAATGCATAGCAACAACCTACCTCCCAAATAAGACTGAATGCTTATTGCCCGGGATAGAAGGTTATAGTAGATTCTGGACAATATAGCAGAACAATAGTTTTGTTAATAGAGGGTCATCGTAAAACCCAATGTGTACGTGTGTGGTTTACCTCTGACAG
Seq C2 exon
ACACCTGATAAAGAGCAGCTGGGGCCGGAGAAGAGCACCATGGACACTCTGGAGCAGATTTGCTCCAAGGACATGGCCAGTCAACACACCAGCTACGACTGGGAACTCTTCATGGCCATGCATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079291:ENSDART00000142328:16
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=0.190
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061714=RasGEF=PU(12.9=57.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGAGTCCAGCTGAAGTTGG
R:
TCATGCATGGCCATGAAGAGT
Band lengths:
223-1261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]