DreINT0124565 @ danRer10
Intron Retention
Gene
ENSDARG00000079872 | rapgef4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:ZFIN;Acc:ZDB-GENE-070912-385]
Coordinates
chr9:2959902-2960351:-
Coord C1 exon
chr9:2960266-2960351
Coord A exon
chr9:2960033-2960265
Coord C2 exon
chr9:2959902-2960032
Length
233 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAC
5' ss Score
7.48
3' ss Seq
CTTTTCTTTTTTCTCTGTAGATC
3' ss Score
12.88
Exon sequences
Seq C1 exon
GTACACTGTGATGTCAGGAACTCCAGAGAAGATTCTGGAGCACCTTCTGGAGACCATGAAACTTGATTGCCAATTCTCAGAGTCAG
Seq A exon
GTATACGTACATAGAGTACGAAATATCATGTAAATACACTGCGAATAAACTAAATGACAATAAGTGGGCCTCAAAATCACTGGGATTTGGATCCCGTTTGACTGTGGACACATTTTATATACACACAGTTCTGTCCAAACAGCTTACAAAAGATGATTTTCCTCACTGTTGCCCTTTAAAAATCACATTAAAATGCTTCATGTTACAAATAGTCTTTTCTTTTTTCTCTGTAG
Seq C2 exon
ATCCTGCTCTGGATGACTTTCTGCTCATGCACTGTGTTTTTGTCCCGAACAGTCAGCTGTGTCCACTGCTCATGACCCAATATCCTTCTTTAATAAAGCCCTACTGCTTTTCAACAAAAACACCACATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079872:ENSDART00000144046:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.033 A=NA C2=0.068
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=PU(25.2=90.0)
A:
NA
C2:
PF0061815=RasGEF_N=FE(36.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACACTGTGATGTCAGGAACTCC
R:
ATGTGGTGTTTTTGTTGAAAAGCA
Band lengths:
212-445
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]