DreINT0124541 @ danRer10
Intron Retention
Gene
ENSDARG00000079291 | rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:ZFIN;Acc:ZDB-GENE-090312-38]
Coordinates
chr23:33502754-33504168:+
Coord C1 exon
chr23:33502754-33502891
Coord A exon
chr23:33502892-33504070
Coord C2 exon
chr23:33504071-33504168
Length
1179 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
ATCTGCTTTGTATGTTACAGACA
3' ss Score
8.94
Exon sequences
Seq C1 exon
TGTTGTATGAGATCTTTAAACCGGATCATAAGGCTGTCACTGTGATGCTGCCAGTTGATGCATCGGTGAACGACATCTTGACTACATTAGTGGATCCTGACAGAAACTATGTGCTTGTCAAGATGAATTCCTCAGGAG
Seq A exon
GTAAATTATCAGATTCATACGATTTGGGTTCAGAGAATCATTTGCCACTCTTTACTTGTTCCAAACCTTTATGGAGTTTTTTTTTTCTGTTAAACAAAATAAGATATTTTGAAAAATGTTCTTTTCCACAGTATTTGTTTTCTATAAATGGAAGAAATTGGTTACCGGTTTCAGCTTTCTTTAAAATATAAACTATGAGATTCATATGATTTGGGATCAGAGTTGGAAATTCTGTCATCATTTGCCCACCCTTTACTTGTTTCAAACCTTTATGAGGTTCTTTCTTCTGTTAAACACAAATTATAATATTTTGGAAAATGTTGGAAAGTTGTAAACATTGACTTCCACAGTATTTGTTTTCCCTAAATGAAAGTAAAAGCTTACCAGTTTTTAGCTTTCTTCAAAATTTAAACTATGAGATTCATATGATTTGGGATCAAAGTTGAAAATTCTGTCACTTTTTCCCACCCTTTTCCAAACCTGTATGTTAAACACAAAAGAAGATATTTTGAAAAATGTTGAAAATCTGTAACTATTTACTTTCATAGTAGAGATAAATATATTGAAGAAAATGGTTAAAGGTGTTCAGCTTTCTTCAAAATATAAACTATGACATTCATATGATTTGGGTTCAGAGTTGAAACTCTGTCATCATTTGCTACCCTTCACTTGTTCCAAACATACCTTTATAAATTTTGATAAACACAAAAGAAGATATTTTGAAAAAGGTTGGAAACCGGTAACCATTGACTTCTACAGTATTTGTTTTTTCTTCTATGGAAGTAAATGGTTATAGGTGTTGTGATTTATTTAAAATATAAACCATGAGATTAATATGATTTGGGTTCAGAGTTGCAAATTGTGTTATTATTTTTAATTGTTTCAAACCTTTTTGAGTTTCTTTCTTCTGTTAAACAAAAGAAGATATTTAGGAAAAATGTTGGAAATCTGTAACTGTTGACTTTCACAGCAATGGTTTCTCCCCTACTAAATGGTTACAGGTGTTCAGCATTCTTCAAAATATTTTCACTGGTGTTCAACAGAAGAAAGAAACTCAAAGATATGTAACTAATTGAGGCTTAGCAAACTTAAATTTTGTATTTTTGGGTGAAATCTTCGTTTGCTGACCTAATCAGATGTTTCATGTAATCAAAGTCTCATCTGCTTTGTATGTTACAG
Seq C2 exon
ACAGAGTCCAGCTGAAGTTGGAGACCACAGCAGTGTCTGCCTCTTTAGGAGTGAACGAAAAGCTTTTCCTCTGCACTTCCAGCCAAGTTGAACAACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079291:ENSDART00000142328:15
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
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTGTATGAGATCTTTAAACCGGA
R:
TTCAACTTGGCTGGAAGTGCA
Band lengths:
230-1409
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]