DreINT0124558 @ danRer10
Intron Retention
Gene
ENSDARG00000079291 | rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:ZFIN;Acc:ZDB-GENE-090312-38]
Coordinates
chr23:33496231-33496653:+
Coord C1 exon
chr23:33496231-33496319
Coord A exon
chr23:33496320-33496563
Coord C2 exon
chr23:33496564-33496653
Length
244 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGG
5' ss Score
9.31
3' ss Seq
TTTTTTTTGTGCTTCTTTAGATC
3' ss Score
11.05
Exon sequences
Seq C1 exon
GTACACGGTAATGTCAGGAACGCCGGAAAAGATCCTGGAGCACATGCTGGAGGCCATAAAACTGGAAACCAACGGAGCTGACTTCATAG
Seq A exon
GTAAGGCAGATGCATGGTTTGTGAGTGACTTGTATAACAACCTGTTATTATAGTTGTGTACCACAGAAGGTCAGACTGAGGGAGTGACCAAAACATTCCAGCTCATTTGGTCTTGTTTACACATCCATTCAAAAGCAGCAGTCAGATGATTGAGGTTGTTCTGGGCTTCTCCACACAGCTCAGTGATGAAAACAAGTCCCTGTTGATGAAGTTTTAAGAGCTTGTTTTTTTTGTGCTTCTTTAG
Seq C2 exon
ATCCCTGTGTGACTGACTTTCTCCTAACGCATCCCGTCTTCATGCCCTGCAGTCAACTGTGTGCTGCCCTCCAGCATCAATATCCTTACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079291:ENSDART00000142328:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=PU(25.9=90.3)
A:
NA
C2:
PF0061815=RasGEF_N=FE(24.1=100)
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:
ACACGGTAATGTCAGGAACGC
R:
GGATATTGATGCTGGAGGGCA
Band lengths:
172-416
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]