RnoINT0124289 @ rn6
Intron Retention
Gene
ENSRNOG00000005271 | Rapgef5
Description
Rap guanine nucleotide exchange factor 5 [Source:RGD Symbol;Acc:1561668]
Coordinates
chr6:145577338-145578515:+
Coord C1 exon
chr6:145577338-145577482
Coord A exon
chr6:145577483-145578417
Coord C2 exon
chr6:145578418-145578515
Length
935 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGC
5' ss Score
6.3
3' ss Seq
TGCCTCCATCCTCTCTACAGACC
3' ss Score
10.67
Exon sequences
Seq C1 exon
CTATTCTGCTAAGAAGTATCAAGGGGAAGAAGAAAACTCAGATGTCCCTTGTCGGAAGCGCAAGGTCTTACATCTGGTTTCCCAGTGGATTTCTCTGTACAAGGACTGGCTGCATGAAGATGAGCACTCAAAGATGTTTCTAAAG
Seq A exon
GTGTGCCAATGCTTTCACATATTTTGGCGTGATTGGTTTTATTTTCAGCTCTGTGCTTCAAAAAAAAATCACATTTTTAGTCATTCAGTTTTTATGTCAAATTCAGTGAAAGTATAAATTCATCTTGACTTCTAAGACCTGGCATTCTGTATATAAGTAGAAACTCAATTTTTAAAAATTTAAATATATTATGAAAGACTATGCATGGAAATTTTATATGCACCAATTTGCGATGGGTTGTTTAAATCGTGGGACTTTTGTGAGTTAAGTAAATTACACCTAAATATACTTTATAATCCGATGCTGTTTAATGTTAAATTTATGATAATGTTAAAATAGTAACATCTACACAGGCAAATAAAACTTAGATAAGCATTTAAGAATCATTTTAATGAGATGTATTTTGTGTCATTCTGTGAATTTTAAATATATGCTATGCTTGTGAATTATATTTGATAATAGGCATTTGACAATATGCTTTGAGAACAGTAACAGTCGCTAATTGATAGTTTGCCATACGTCTCTATCACAGACAGTTCTCTGGAATAGAGCTTGATATTGGTGCCTTTTAGGCATCCAGTTAAAGACTTATCTATCCCTCTGCCTTAACTCAGGTTATCTTTTAAGCCCACTGGTTATTTTCATATGATTTCCTCCCAAGCAGTCCTGCAGGGATTCTGTTTTGAGATCTAAACTACTTGTGGAACTCTCTAGTAACCAACTAAGATTTGTTTTCAGCATATCCTATAGACAGTCTTTAAAAGTAGCCAGGTTGTTGAGTGGCTGGAGTCCACTTTCTGGAATGAGATAGCCATGACCTGAGCCATGTGTTTGACCACTGAGCTGTATGGCCAACCCTGTCTCCATTGAAATCCTTACGGAGTCGACACTGAATTGTTACATTTGCGGTTTTGTTGCCTCCATCCTCTCTACAG
Seq C2 exon
ACCATATACAGGAATGTGCTGGATGACGTCTATGAATATCCGATCCTTGAGAAAGAGCTGAAGGAGTTTCAGAAGATACTGGGCATGCACCGCCGTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005271:ENSRNOT00000007112:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=FE(43.6=100)
A:
NA
C2:
PF0061815=RasGEF_N=PD(5.5=18.2)
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:
CTATTCTGCTAAGAAGTATCAAGGGG
R:
GCGGTGCATGCCCAGTATC
Band lengths:
238-1173
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]