RnoINT0124264 @ rn6
Intron Retention
Gene
ENSRNOG00000001516 | Rapgef4
Description
Rap guanine nucleotide exchange factor 4 [Source:RGD Symbol;Acc:621886]
Coordinates
chr3:58894044-58896064:+
Coord C1 exon
chr3:58894044-58894190
Coord A exon
chr3:58894191-58895966
Coord C2 exon
chr3:58895967-58896064
Length
1776 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACA
5' ss Score
8.1
3' ss Seq
CATGCTTTTTATGTTCACAGAAA
3' ss Score
8.99
Exon sequences
Seq C1 exon
TTTTGTTCAAGGTCTACTGCATTGACCACACCTATACCACCATCCGAGTGCCTGTAGCCGCCTCGGTGAAGGAAGTCATCAGTGCAGTAGCAGACAAACTTGGCTCTGGGGAAGGCCTGATCATTGTCAAGATGAACTCTGGAGGAG
Seq A exon
GTAACAGCTTAGATTAACACTGTGGGCTTTTCGTGAAATAAGTCATCCTGGCCAATCAAAACCATCCAAGGAACAACGGAGTCCATTCACAGTGACCAGAAGGATGCCAGAGGTTGTTCGAGCTCCCAGGGATAGCAGAAATATTGTGTGAAGAGGCTGGCTTATGAAATGTCTAACATCCCCTATCTAATAGATTCCCACGTAAAGGAGTGAGAAGTGATTTATGGGAGACAGCTGCAGTCTCCGGCATCCGTGTCAGCCTGGGGCTCTTTCAGTGGAAACACAACAAACTCTCTGGGCCTCAGATCTGGGAGAAAGGTGCACCTTCAGGGGGCATCAAGTTTGACAAGCAAAGACTCCAGGTGCCCGCAAACCTGCAGCTGGGGTGGTGGGGGACGAGTTCTTTTTAGCCGATGACAGTTTCCCCACTTGCCCAATAGAGCTCAGCTGCTCTATAACATGAGGGTTGTTCAACTCCCTAACCTGGGACTAAAATTCCTTTCCTCTCCCCTGACTATAGTTACCCTCATTTTGTATCATCTTGTATGGCCTGACCACTTGAATGTAGCAATGACAGAAAAGGATACATTAGACACACTGTGTGCTCCTGAGTTGCTCCCAGGCCCTGAGGAGCTGGGAAATAAAGGAAACCTACATCCCACGCTGGCAGGGGTTTGAGCAGTGGTCACCCACAGTGCAGGGAGGCGGCTCAGGAAGGAGCCCTTAGGTTAACTCCCCAGTGATGGCTTCACAGCCCTTTGAGGGCTCCTTTAGGAAGGGAGTGAAGCACTTCTGCCTTGTCTGAAAGTAGATGATTCTGCTGATGCAGGATTTTAGAGTGGATGATGGATTCTCAAGACCACTTCCCCTACTTTCTGCCAGTTGTTCCGTACCCAGGATGGCCTCTGAGATTCATTTGTTGCCTCTTTCCCATAGGCGTCCCAATATATCAGATATCCACCTAAACGATAGGGTGCCACTGAAGCCTGCCCATCGATGTCCCATCTAAAGTTTTAACTGTTCCCCTGACACATACCTTCTAACCCCCTTCCCTGCTGTGCCTTGTGGCCCTTGTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCTCTCTCTCTGTCTCTCTGTCTCTCTCACACACACACATTCCCTATCCCCTTATCCCTCTATGTTAACTAGATTTTTAATTTATGTTTTATCTCTCTGTATCATTTCTTTATGTGTCCCTAGTGTCTGGTATATGCTAAATACTAAAACATATTCAACAAATGGATTTGTAAAATATAGAAAGATACTTAAAGTAGTTTCCTATTAGCTTCTTTCCGTAATGGGCACAAGTAAAAATAAAAAGATATTTTGCAACTAAAAATCATGTGAGATCTCTGAAGTGCCCCCCCCCCAAGGTTTCTAATAATGACCTTTCTATCTCCAGCTTACCAGTCATTGTTGCCATCAAGAAACCTAACTTGGTATCTGAATGACTATGTGGGTTTTATAAATAATTATGGTTGCAGAGTAGATCTGGGCAAATTGATCCTTGGCTGTGCCCGCTCCTGTTGTGTGGTCATTTCTGATGCTGTCCCGAGTACCGTGCTATACAGCAAGCACTGTCTTTTATTCAGCAGATCCGTTCACTCCTGTGTTTTATGCAGTCCCATTGCATGTTCCGGTAATTCACCAAGCTGGCAATTTGTTGGTGTGATTAGGGCAGTGCAGCAAATCTCAGATGGATTTAATAGGCAATCTCATGCTTTTTATGTTCACAG
Seq C2 exon
AAAAGGTGGTGCTCAAACCTAATGATGTTTCAGTATTTACGACGCTCACCATTAATGGACGCCTGTTTGCCTGCCCGCGAGAGCAATTCGACTCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001516:ENSRNOT00000010630:26
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:
PF0078818=RA=FE(61.2=100)
A:
NA
C2:
PF0078818=RA=PD(35.0=84.8)
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:
TGTTCAAGGTCTACTGCATTGAC
R:
AGTGAGTCGAATTGCTCTCGC
Band lengths:
241-2017
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]