DreINT0124610 @ danRer10
Intron Retention
Gene
ENSDARG00000074307 | rapgef5b
Description
Rap guanine nucleotide exchange factor (GEF) 5b [Source:ZFIN;Acc:ZDB-GENE-061215-2]
Coordinates
chr16:19330453-19330810:+
Coord C1 exon
chr16:19330453-19330531
Coord A exon
chr16:19330532-19330660
Coord C2 exon
chr16:19330661-19330810
Length
129 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
GTTTTATGTGTGTGTTTCAGTGC
3' ss Score
10.45
Exon sequences
Seq C1 exon
AATAAAGCTCTGTTCCACCAGCTCAGTCTGAAGGAGAGCTGGCATCCCATGAGGGGACCAGAGAGAGAGAGGAAAGAAG
Seq A exon
GTAAGCTCATAAAATATTCCTCTCATTTTTCTCTCATCACTCTCCGACTGCCTGCAGAGCTGCTGGAGATATTGGCAGATTCTTCATTAATAACAGCATGAGAAATCTTGTTTTATGTGTGTGTTTCAG
Seq C2 exon
TGCTGTGTCGTGTGTACGTGACCGTCGACTCGTATGTTAGCGTGAGGACACACAGCGAGGTGTGTGTCCAGGAACTTCTGAGGGCTGTGGCTGAAAGACTGGACTGTGCTGAAGATGACATGGTGCTGATGGCCCTCACATATCCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000074307:ENSDART00000114954:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAGCTCTGTTCCACCAGCTC
R:
CTCCAGGATATGTGAGGGCCA
Band lengths:
226-355
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]