DreINT0017703 @ danRer10
Intron Retention
Gene
ENSDARG00000075924 | RAPGEF4 (1 of 2)
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:HGNC Symbol;Acc:HGNC:16626]
Coordinates
chr6:6748946-6749340:+
Coord C1 exon
chr6:6748946-6749031
Coord A exon
chr6:6749032-6749261
Coord C2 exon
chr6:6749262-6749340
Length
230 bp
Sequences
Splice sites
5' ss Seq
CAGGTCATT
5' ss Score
4.45
3' ss Seq
TGCAAATGTTTCTCCCGCAGATC
3' ss Score
11.77
Exon sequences
Seq C1 exon
ATACACTGTGATGTCAGGCAGCCCTGAGAAGATTCTGGAGCATCTGCTGGAGACAATGCGACTGGACATTCATTTCTCTGACCCAG
Seq A exon
GTCATTGACTAATCGTAACATACAATAGTTGAAAAGCAGTTGTGCCTATAAAATAAAAATGGTTAGTTTTAAGTACTAGTGTTTCATTAATGTGCTATTCATCTTCATTCACCAATAAGATTAAGAGTTTGATTTGATCTGATCTACAGTATAGATATTATTATCATTTAAATCATCTTTCAAAGCTGTATTAGTGCATTTGAATGATTCTGCAAATGTTTCTCCCGCAG
Seq C2 exon
ATCCAGCTCTTGATGACTTTGTGCTCATGCACTGTGTTTTCATGCCCAACAGTCAGCTGTGCCCCGCTCTTCTGGCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075924:ENSDART00000166607:15
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=PU(24.8=90.0)
A:
NA
C2:
PF0061815=RasGEF_N=FE(23.9=100)
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:
TACACTGTGATGTCAGGCAGC
R:
CAGAAGAGCGGGGCACAG
Band lengths:
159-389
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]