RnoINT0124273 @ rn6
Intron Retention
Gene
ENSRNOG00000001516 | Rapgef4
Description
Rap guanine nucleotide exchange factor 4 [Source:RGD Symbol;Acc:621886]
Coordinates
chr3:58920485-58924038:+
Coord C1 exon
chr3:58920485-58920539
Coord A exon
chr3:58920540-58923913
Coord C2 exon
chr3:58923914-58924038
Length
3374 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
TCCTGCTATTCTTTTAACAGATC
3' ss Score
10.21
Exon sequences
Seq C1 exon
CGCATGATTGCAAATACTGCCAGAACGGTGCGCTACTACAGGAGCCAGCCATTCA
Seq A exon
GTAAGTTCTGCATGCCGTCATGGACATGGTGTGATTAAATCCTTTTTAATGAGACTTTCAAGACACTCCAGGAGTCTGGACAGCATTTGACACAGCTTGGACCATGAGACCCATGTGTGCCTTGGGTTTAAGAACTTTGCTTTGCTGTCGTAAGGCTAAACTGTATTTGCATTATAACTCCAGAAAATAGTGTCAGGATTTTATTTTAGTAAGTGAGCTTGAAGGAAATGCATTTGTTCATGTCAGGGTAGCCAGAACAGGTAGGTTGCAAAGGCCCACATAAGCCTGCTTCCAAGCTGTCCCCAGCGTGACTCACGCTCGATGCTGAGAAGCCCGGCAGCTCTCTGTGAGTCAGTACTATTGTTTATAAACTGGGAAAGGTAATATTTATCGTCTCCTGAGTATGCATGAATGTTTACAGTGCTTTTGCTAAAAAGCCTATGGCAGGGCTCTATATAACATTTTCAGTGTTCCCGGGTGTATGCCGTGAACACCGTGCTATGTTTTCACATCTATGAAATATTACTATTGACAAATGGCCATTTTAGCCTGTTGGGTGCTGCCGTCTCCCCGGGCCTAGAACTTGGGATAAGGACCAGAGCTTTGCAGCTCCGGTCTGGTTTGGGAGAAAGCAGGTGAACCCTTGGAAGTTTTGTGCTAATGTCATTATGGGAGTCATTTTGGAGAACTGACATCGGTATAAGATGACACAGATGTGACAGCACCATCCTCTCCAGAAGAGACTGACAGGTTCTCGTTTTAATAATCACAGTGGTGTGCTCTTTGTAGTGTAGCTCTGGCCCAAAGCCAGAGCTTGCTAACCCAGAATGCCAGGACTCCTCTCCTCCTCCTTTCCTCCTCCTCTCTCTTCTTCTCTCCATCTCCTCCTCTCCTCTTCCTCTTCTTTCCTCCTCCTCTTCCTCTTCCTCTCTCTTCCTCCTCCTCCTCTTCCTCCTCCTCTTCTCTTCCTCTTCTTCCATCTTTTCCTACCTCCTTCTTCTCTTTCTTCCCTCTTCTTCCTCCCTCTCCTCTTCTCTTCTTCCTTTCCCTTCCCTTTCTTTTCTTTCTTCTTTCTTCTTCGTCTCTTCTCTTCCTCCTATCTCTCCTCGTTCGCCCTTTCTTCTCTCTCCTCTTGTCTTCTCTTTTTTCAATGTTTCAAATAAAATGTAAAAGAAAATAGAATAATCTTTGTGATAAATTAGTTTTGGTCTTAGAGAGTGGACGTAGTAATGAGGCGGTGTGATAGAGGGTAATTCATAATCGACCATAACGCCTCGGCGTTCTAAGAAAAATGAGAAGGGTCTTTTCCTCCTCCTCCTCTTCCTCCTTTCCATGTTCAAGAGAAAGAAAGAAAAAGAAAACCAGAGAAAGTAGTTTTGGCTTAGAGAGTGAGAAAAGCTTTAAAAGTTAATTCAAACAACCACACCCTCCGGCTTCTAAAAAATGAGAAGGGTCTTACATGCCACCACCCCTTTCTTTCTACATGGATTCTGCCAGAATTCAAGTATCTCATATCTTTTCCTATAGTAATGTGCTTTGTGTGTAAAAGACATAGCCATAAATCAACTGAAAAGGAGGAGAAGCAGTACCAGTTACAACAAGCTTATAAGCCAGAATCCATGGCCCTTCAGGGGATTCCAAGACATTCTCGAAATTACATGCAAAGACTCCTATGTGCTGAAGAGGGCTCAGAGCCTCGAGGAGGGTTCTCAGGGAGGTTCCAGAACCAAACAGAAGCAGTGGTAGCTTTGTTTCACCAGCCTCTTTGGCAGTAAATTCTACATTCTTCCACATCTTTAAGGAAAGTGAGGAGATTTTTTTTTTTAATTTTCCACTGCATTTGTTGAACTTATCAGCAAGTGCTGGTAAACAACAGCTGCTGGGCTCTGAAGTCAACAATCTATAGATAAAGCTATAGGAATAGATTCATAAACATCGTGGGGCTATGTACAATGTAATTACAGTATATTGTACACGCAGAGTACACTGCCAGTGGCAAGCGGAGGAAATTAAGCACAATGTGTTCTGTGCTTCACTGTGGTATTATTGATATGTGATAATTACCCTGATGAGTTTCTTCTTACAGCGAGCAGGGGCCTTTGTGGCTTGTCCCTGCTTTCTGTGCTCTCAGACCTGCTTCACTCCCCTCCAGCCCTTTATGCAGATGGCGCTCTAATTGTTGTGCGGAGTAGGGAGTGGAGCTGACAGGAACAACCGGACTTTAGAAAGCAGCGTAGGGGTGGGAGGGAAGAGCTCTGGTCCAGAGTCCAGATTCCAGCTCCGCCACTCCTGCATACTACTAGGGAAGGGAGTGACCCCAGGAGAGTGACCCCTAGAGTTCAGCAGAGGGCTGGACTATGTATAAACAACATTTCCTTCTTTGTATGGAAAGCCTCAATTTAAAATTTGGAGAAATTTACAGGGAGACATTTAGATTCCCTGTTTCAAAAAGAAAGAGAAGGGGGGGGGGGGGGAGGTAGGAAGGAACAACCAGAAGCAAAGCGAAGTCCGGCCGGCCATTCTGGACAGATCCCTACACGATGATGGTGGTCAGGAGCCTGGTAACCACTTCCTGAGATACTGTGCTTCCAATTTCCAGCTCTGCTATTGAATCTGGCCTTCCTCCTTCTTATATTATATGGTGTGTAGGAACTATACAAGTTAGATTTTCTTGGAGTCCTGGTTTGAATAAAATCCACCTACCTTTTTGATAGCCCAAGTATTCACATCCATAGATAAAAATAAAACAGTCAGTGGACTTTCAGAGCAAGTCATGTCAGAGAAGAAAAGTTTACTAGAAGTCACCAATTAGCCAGAAGGTATCCTTACTCCAATTCGAGCTGTGCCTAGGGACATACAGCTGGAGTGGTACTGTATGTGTATGCAGGCAGAGGGGGCCTACGAGGCCCGAGGCCCACTGGCTGGCTTCAGATCAGACGTGGTGTTAAGTGCTTTTCCGAGTTGCTAATGAAGCTCCATCTTTGACGTTAGTCCTCATCTGGATCAAAGGGGGTGGAGACAGAGTATGAGACACAGAGGTGAGCTGGGAAGGGAAAACAATTTTCATCTGTCACCAGGGCCATCAGACGGATGCTTCCCTTTTTATTTGGTGCCTTTGTGTGTATATGTGTATGTGTGCGCAATACAAAGGAAAATGATCAAAAGAGATGATTCCAGGGAGAAAAGAAAATTGGAGGGTAGGTGGAAGTAGATGGACCAACCAAGTAGAAATATTCCAGTGGAATGGTGTGTGGAAAGGTCTTGACAGAACCCAGGGAATCGATGATAAATGTAATAAGTCAGTGGGGGGAAGAAAGCCGCATCTCACATGCAGATATTACGCAATGCCAACTCTCCTGCTATTCTTTTAACAG
Seq C2 exon
ATCCGGATGCTGCTCAAGCTAATAAGAACCATCAGGATGTCCGGAGTTATGTACGGCAATTAAATGTGATTGACAACCAGAGAACTTTATCACAGATGTCACACAGATTAGAGCCTCGCAGGCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001516:ENSRNOT00000010630:34
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.105 A=NA C2=0.690
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PD(0.5=5.3)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]