DreINT0124480 @ danRer10
Intron Retention
Gene
ENSDARG00000043593 | rapgef1a
Description
Rap guanine nucleotide exchange factor (GEF) 1a [Source:ZFIN;Acc:ZDB-GENE-081105-26]
Coordinates
chr8:11751793-11752064:-
Coord C1 exon
chr8:11751980-11752064
Coord A exon
chr8:11751886-11751979
Coord C2 exon
chr8:11751793-11751885
Length
94 bp
Sequences
Splice sites
5' ss Seq
TAGATATCC
5' ss Score
-3.12
3' ss Seq
TTGCCCTTGACTCTGAACACGTA
3' ss Score
0.32
Exon sequences
Seq C1 exon
ATCGGGTTTTATACTGTGAAGCTTTCTTGACCACGTACAGAACATTTCTAACCCCAGAGGACCTCATTAAAAAGCTCCGCTATAG
Seq A exon
ATATCCTTTCTGGGAAGGTTGCATTATAAGTCTTTGCATATCTAACCTTTGTACACCAAGCATTTTTTTCTTTTTTGCCCTTGACTCTGAACAC
Seq C2 exon
GTACACCAGATTTTCTCTCAGCTCTGACAGCATCAAACAACGAGCTAGTAAAAACACCTTCTTCGTGCTGGTGCGTGTCGTGGATGAGCTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000043593:ENSDART00000139947:15
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:
PF0061815=RasGEF_N=FE(24.8=100)
A:
NA
C2:
PF0061815=RasGEF_N=FE(27.4=100)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTGTGAAGCTTTCTTGACCACG
R:
CAAAGCTCATCCACGACACGC
Band lengths:
167-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]