DreINT0124536 @ danRer10
Intron Retention
Gene
ENSDARG00000079291 | rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:ZFIN;Acc:ZDB-GENE-090312-38]
Coordinates
chr23:33496564-33497166:+
Coord C1 exon
chr23:33496564-33496653
Coord A exon
chr23:33496654-33497023
Coord C2 exon
chr23:33497024-33497166
Length
370 bp
Sequences
Splice sites
5' ss Seq
ACAGTATAT
5' ss Score
-1.37
3' ss Seq
CTGCTCTTGCACTTACCAAGCGG
3' ss Score
1.49
Exon sequences
Seq C1 exon
ATCCCTGTGTGACTGACTTTCTCCTAACGCATCCCGTCTTCATGCCCTGCAGTCAACTGTGTGCTGCCCTCCAGCATCAATATCCTTACA
Seq A exon
GTATATTAGTCACTTATATTCTGCTTCATATTGATATTTCTCTACCAGAACATTTACATGAACATCAACATTCTCTATTAAAATAATACTCTGATTACAAGGATAGTTCACAAAAAAGACAATTCTGTGATCATTTACTCACCCTTGACTTGTTCCAAACCAGTTAGAGTTTTTGTCTTCTGTTGAACACAAAAGAAGATATTTTGAGGAATGTTGAAAAACGGTCCACTGAAATTCATTGTAGAAAAAAAGTTCTATGGAAGTCAGTGAACATGGTGAACATACCCGACAACACTCCAGTTTTTCTAGAGAGCTAAGAGCTGTTTGTGATTGTTTTGATGTTCCTTAACCTGCTCTTGCACTTACCAAG
Seq C2 exon
CGGAGCCGTCTGAAGGCTCAGACCTGGAGAAGGCAGCGTACGCTCTCAACACCAAGCAGAAGGTGGTGAAGCTGGTGTGTCACTGGGTGGCTCTGTTCGCTCTGCTGCTCAGGGACGATCCTGTGGCCTCTGAATTCCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079291:ENSDART00000142328:10
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=0.015
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=FE(24.1=100)
A:
NA
C2:
PF0061815=RasGEF_N=FE(43.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTGTGTGACTGACTTTCTCC
R:
TCCAGGAATTCAGAGGCCACA
Band lengths:
230-600
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]