RnoINT0124184 @ rn6
Intron Retention
Gene
ENSRNOG00000014316 | Rapgef1
Description
Rap guanine nucleotide exchange factor 1 [Source:RGD Symbol;Acc:619793]
Coordinates
chr3:8291970-8293573:+
Coord C1 exon
chr3:8291970-8292081
Coord A exon
chr3:8292082-8293497
Coord C2 exon
chr3:8293498-8293573
Length
1416 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CTCATGCTCTTTTACTCCAGGGT
3' ss Score
8.25
Exon sequences
Seq C1 exon
GTCCCCGAAGTCACTGGATGCTCTGGAGTCAGCCCAGTCAGAAGAGGAAGTGGATGAACTGTCCCTCATTGACCACAATGAAATCATGGCCAGGCTGACACTCAAGCAAGAG
Seq A exon
GTGAGGTTTCCCCAAACCTGGATCTTATAACCACCAACCAAGAGGGAAGGGAAGCAGAGAAATGCTCCAGTGGGGAGACCTGAGTCAGGCAGCGCCTCAGCTCTTGGGTCCCAGCTAAAAAGGGTTTCTGGAGAAAGCTTACTGTCCCTTTCTTTCCAGAAGTGAACTTGGCCCGTACAAAGCCTCTTTGAGACTCAAGCAGGTACTTCTGAGGGCATTGCAAGGCTCAGTGTAGCCTGTACAAGAAGCAGTGTGAGGCATGTGTGTGCTCTTAGTAACACAGCCCCTCCCCCTTCTGGTCTCTGCCCGTTAAGAAAATGGGGCATAGATGCTGATCTGTGCCTTGTTTGAGGAGCCTTATTGATAAGAACAACACCCAGACATGTCATGAGAGAGGAAGAAACTGGCCCCAAGAGCTTTTCTCTTCTCTGTACGTTCTAGGAACTTGGGTTAATGGGACATCTCGACCTCTGAGTAGCTCTGCATTTGGGGACTGGGTTGATGGTTGTAACATACAGACATAGGAAAGGTACTCCCTTATGCAATTCCTGGGCCATCCTGAGCGGCTTCCTAGGCCATCAGGCTGCTGGTAGGGTTAGCAGAATCTAGGCAGAACCTCTGCAGAAAGAAAAGCTAAATTCCTTCTGGAAAACAGGGTCATGAACATAGCCAACCTTGTCCCGGGTGGGAAGCCCAGAGCACTCAGAACTCTGAAGTTCAGATGGAAATATCTGTCCATGGGGTGCGCAGATAGGACATTGGCTCTGTCTCCCTCAGAGTCCCAGCCCCACCTACAGCTCCGTCACTAGACCAGACTAAAACTCGTTTGCCTGTGGAAAGAGTTGGCCTTCCACTAGCAGCTGGGTTTGGTTACCTTGTAAACATCCTATGTCATGAGCAGTCTTGTGATGTTTTACACTCTACTAGTGAAGTCCTCCTGAGAACAGCCTGTGGGGTATGTCCCTGCAGATGAATCCTACTTCCACCTTGGAAAGGAGCTAAACCCAAAGGTAGCTGCAGGAGTGGAGAGACACAAGCCTGCATATCATCTCCTGTCTCCTAGGCCTAGGAACTGCCTTTTTCCTCTGGAATCTCACCTTTCGGGGTGAGCCACGAGGTGGAGATAGGGTTGAAACCATAGTGCCCTGACCCCATGTGGCCTCTGGAAAGTGATGTACCCTGGTGCTCACAGCATCTGGGCAGCTTCCTTAATGCCCAATTTCCTGTAAGAGTTCTGAGCAGTACCATCTACAGAATCCATGGGAGCAGGGCTGCAGATGCTGTCTGTGTGCACAGTCCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGAACTGAGGGGAACAGAAGGGGCTCGGGGACCCTGAAGCATGGGGAGTTCATCACCTCAGCCTTGCCTCATGCTCTTTTACTCCAG
Seq C2 exon
GGTGATGATGGACCAGATGTTCGTGGAGGTTCAGGAGACATCTTACTGGTCCATGCTACTGAGACAGACAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000014316:ENSRNOT00000060977:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.825 A=NA C2=0.385
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061815=RasGEF_N=PU(20.4=76.9)
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:
CCCGAAGTCACTGGATGCTCT
R:
TTCTGTCTGTCTCAGTAGCATGGA
Band lengths:
182-1598
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]