DreINT0124487 @ danRer10
Intron Retention
Gene
ENSDARG00000043593 | rapgef1a
Description
Rap guanine nucleotide exchange factor (GEF) 1a [Source:ZFIN;Acc:ZDB-GENE-081105-26]
Coordinates
chr8:11743920-11744432:-
Coord C1 exon
chr8:11744331-11744432
Coord A exon
chr8:11744018-11744330
Coord C2 exon
chr8:11743920-11744017
Length
313 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGT
5' ss Score
7.7
3' ss Seq
AACTGATGTTGTCTTCACAGGGT
3' ss Score
8.32
Exon sequences
Seq C1 exon
CACTTAAGGAAGCTCAATAACTTCAACTCATACTTGGCAATATTATCAGCGCTGGATTCAGCTCCTATCAGAAGACTGGAATGGCAGAAGCAAACGTCTGAG
Seq A exon
GTCAGTTCAATTCAAGTTTATTTGTATAGCTCTTTTCACAGTAATTATAGTTTCAAAAGCAGCTTTACAAAACATGCACATTAATGCATTAAAATCAAATTTGGAAAAATTTGTGTTATTAGATACTATAATTTCGTTAGTTAGTAATAACTTTAACTAATTAACTTGTAACTAATAGCTTTAAACAGTTAATGTTGTTGTATATAAGCATAGTTAACGTGCAGTTATATAGCATACAGGTGATGTCTCATCTATGCATCACTGACCCTTGTTTCTCAGATGATGGTCACTGTAACTGATGTTGTCTTCACAG
Seq C2 exon
GGTTTGGAGGAATATTGCACTTTAATTGACAGTTCGTCCTCTTTCCGGGCGTACAGAGCAGCTTTGGCAGACGTGGAGCCTCCATGTATACCGTACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000043593:ENSDART00000139947:21
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:
PF0061714=RasGEF=FE(19.1=100)
A:
NA
C2:
PF0061714=RasGEF=FE(18.5=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:
CACTTAAGGAAGCTCAATAACTTCA
R:
AGGTACGGTATACATGGAGGCT
Band lengths:
200-513
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]