RnoINT0124254 @ rn6
Intron Retention
Gene
ENSRNOG00000001516 | Rapgef4
Description
Rap guanine nucleotide exchange factor 4 [Source:RGD Symbol;Acc:621886]
Coordinates
chr3:58866313-58866877:+
Coord C1 exon
chr3:58866313-58866389
Coord A exon
chr3:58866390-58866730
Coord C2 exon
chr3:58866731-58866877
Length
341 bp
Sequences
Splice sites
5' ss Seq
AAGGTATAA
5' ss Score
7.08
3' ss Seq
GACTGTCCTGCTCTCCCCAGGGT
3' ss Score
10.48
Exon sequences
Seq C1 exon
TGTTTAACCAGGGGGAAGAAGGTACCTCCTGGTACATCATTCTGAAAGGATCCGTGAATGTAGTCATTTATGGCAAG
Seq A exon
GTATAATATATCTATCTGTATCTTTTTCTTTTTGAGGCTTTATTATACACCATTTGCTAGTGTAGCTCTAAGTAGTAACAAATGTTGCTGCAAATAAATTTACCATGGCATTGTTACTCCACGTAGAAAAGACATAATTTCATCTTTAATCATACATTTCCTCAATTATTGCACTCAGAGTCATTCATTGACTGTGTTTATTCTGTGAAAGAAATATGAAGCATTTTAATCTGATTATAACACTAATGCAGTCCACTCACAGGCACGGTGTTTGGTGGCAGGGGAGGGGAAGGAGGGTTTTTGGTCCCTTTTTTTTTTCCTGACTGTCCTGCTCTCCCCAG
Seq C2 exon
GGTGTGGTCTGCACCCTGCATGAGGGAGATGACTTTGGCAAGTTAGCTCTGGTGAACGATGCTCCGAGAGCTGCATCCATTGTTCTTCGGGAAGATAATTGTCACTTCCTAAGAGTTGACAAGGAAGACTTCAATCGGATTCTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001516:ENSRNOT00000010630:17
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:
PF0002724=cNMP_binding=FE(28.7=100)
A:
NA
C2:
PF0002724=cNMP_binding=FE(55.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTTAACCAGGGGGAAGAAGG
R:
CCTCAGAATCCGATTGAAGTCTTCC
Band lengths:
224-565
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]