RnoINT0124248 @ rn6
Intron Retention
Gene
ENSRNOG00000059961 | Rapgef3
Description
Rap guanine nucleotide exchange factor 3 [Source:RGD Symbol;Acc:621869]
Coordinates
chr7:139245118-139245717:-
Coord C1 exon
chr7:139245571-139245717
Coord A exon
chr7:139245231-139245570
Coord C2 exon
chr7:139245118-139245230
Length
340 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCCA
5' ss Score
3.41
3' ss Seq
CGGTGTGGCTCCTCCCCCAGGAT
3' ss Score
8.73
Exon sequences
Seq C1 exon
GGGCTGGTGACCACGTTGCACGAGGGAGATGACTTTGGACAGCTGGCTCTGGTGAACGACGCACCTCGAGCAGCCACCATCATCCTTCGAGAAAATAACTGTCACTTTCTGCGTGTGGACAAGCAGGACTTCAACCGCATCATCAAG
Seq A exon
GTGCCATAGTTTTTGGGTGGGAGTGTTTGGGGGTGGTGAGAACATGGTGGGTGTACGGGCAAAGGCGCTGGCATCAGAGAGAATTTGTAAGGAAACTTGGCATCTGACTGGTGTCATCTGACAGTTTGGTGTGAGAGACCAGGGACTGGCAGGTGAGGGGCGGGGATTGAGGGGGTTGGGTCTGTGGAGGCTCTGAGACTGAGAGATCTGATACAGGTGTATCTGGAGAAAAGCGGGGGCTCCTTAGGGGCCTCTAGGGCTCCAGACTTGGAAGGGAGGTAGTACAGGAGGTCTGGCAAGCAGCTCAGTGTGTTAAGCATCGGTGTGGCTCCTCCCCCAG
Seq C2 exon
GATGTGGAAGCAAAAACCATGAGACTGGAAGAACACGGCAAAGTGGTGTTAGTTTTGGAGAGAACCTCTCAGGGTGCTGGCCCTTCCCGCCCTCCGACCCCAGGCAGGAACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000059961:ENSRNOT00000078644:9
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=0.500
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=FE(56.5=100)
A:
NA
C2:
PF0002724=cNMP_binding=PD(2.4=5.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGACCACGTTGCACGAG
R:
GGTTCCTGCCTGGGGTCG
Band lengths:
254-594
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]