RnoINT0124182 @ rn6
Intron Retention
Gene
ENSRNOG00000014316 | Rapgef1
Description
Rap guanine nucleotide exchange factor 1 [Source:RGD Symbol;Acc:619793]
Coordinates
chr3:8287570-8289335:+
Coord C1 exon
chr3:8287570-8287665
Coord A exon
chr3:8287666-8289249
Coord C2 exon
chr3:8289250-8289335
Length
1584 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGT
5' ss Score
8.57
3' ss Seq
CTCCATTCTTCTCTTTGCAGGAA
3' ss Score
11.19
Exon sequences
Seq C1 exon
AGTGAAAACGCCAGCAGTGAGGAAGCTGGTGGGGGTGAATATGTCAATCTGTACTCCTCTGGCCAGACCAGCGAGGAGCTAGCTCCCTCTGGAGGA
Seq A exon
GTAAGTAACCTCACTGGGTGGCCTTGTGCATGGGCTGGCCACTGTCCCCCTCAAAGTCGCTTCCCTTGTAGCTGCTTCTATTGGCTGAGCCCCTGTAGGCCTGCTGGAAGCCAACCTGTCCTGTGGGAGAGGACATGGCTTCCAGGTCAAGGTCTGCCCTGCTTTTGCTTCAGTGAGTGTGGCATTTCTCAGAACCTAGCTGATGAGTCTCCTAGAAACCACTGGCCCAGCCCCAGCTGCTCCCTGGAATTTCTTCCCATTCATCCCTCAGTGCTGATCCCCTTGTCCAAGAGATGCTTTTCACTCCTGCCCTTCAGTTTTTCCCAGCATGCCCTGCTGCCCTCAGCTACTCCCAAGGAAGCAAGGCCAGTGATGGGAGCCCTGCTGGATATCCACACTTGTCCCTCCTGAGAGCAGGCTCCTTGCTGGGTTCTGGAGGTCCATGCCTGGATTATGCCACTGCCCAGATGGTGGCCTCACATTGCAAACCTTCTATTGAGCAGGCAGCTTTCCAAATTTGGCTTTAGCAAAACGGGCAAATTGAGAGATTTCAGACGTCACCTTCATGTGAGACTGAATGAGAAGTTCCTTTGGGAGATGAAGTCAGAGGTCACTGTCCCCAGGAGATTGAATGAGAAGTTCTAGGGGTGAGGTCAGGTCATCATGGACAAGAAATCACCGCCCTGGCAAGCCCAGACTGCACATCATGGCCATCCCATGAATAGTCATGCCATGATTCCTTAGGGCTTTTCAATGTCTATGTCAAGGCAGCCACCGCCCCCCCCCAGACATCAACACAGCGTAAGCTTCCCTCCAGTGGGATTTGGTCCTGTTTGTGATAGTTGAACCAGCTCCCCACCCACTGGTGACCTGTGTCACTAGTAGCACCAAACTCAGGGAGTCAATGCCCAGGCCCCACGGCCTTCTCTGCCCTGCAGTGCCAGCCCCACTGTGCTGTCTCTGGTGACAGTCCCAGGATTCACAAGGCCTTTTTCTTCACCACCACTTCCAGGACAGCCCAGAAACACTGTAGACGTGTGTTGTCAGTGGGTACAGAGGCAGCAAGTCTGCCCAAGACAGGTTACATTCGGAGTTTAGGCATCTGGACTTCTGAACTGGCCTGTCACTGGTTAAGGGTCATAGCCCTGAAGACTGTGAATACTGTGTAAGAAGTCGGGGAAGTTTGGGTGTAGTGGTTAAAGATATAAGCTTGGGGGGCAGATAGCCTCCTAAGAGTTCAAGTCTACTCTGCCATTGGATATCCTGGCAGTCAGTTTCTGCGGGGAATGGAGGCATGGTGGTAGCTTGTTGAAGAGAGTGAAGGAGAGGTGTGCAGATACTCAGCACTCTGACTTCAGGGAGTGGATACAGTGTCTCCACCCCTGCTGGCAGGCCTTAGACAGTAGAAGGAATGGCACCTCCCCCTCCAAAGGCAGGTGTTGTTCTCCAGAGGGCCTGTGTTTCTAGTAATTAACCCCATTCCTCATTAGCTTGTTCCCACGGCCAGCTGCTCCATAGTGCTAAGGCGACAGACCACCCCAGCATAGGCCGTCTGTCCAAACGCCTCCATTCTTCTCTTTGCAG
Seq C2 exon
GAACCGCCATCTGGGAAGGACGGACATCCCAGAGATCTTTCGGTCAGCAGTGCATCTGGGAAGGACAGCAGAGAAAATGGGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000014316:ENSRNOT00000060977:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGAAAACGCCAGCAGTGAG
R:
CTCTCCCCATTTTCTCTGCTGT
Band lengths:
182-1766
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]