RnoINT0124255 @ rn6
Intron Retention
Gene
ENSRNOG00000001516 | Rapgef4
Description
Rap guanine nucleotide exchange factor 4 [Source:RGD Symbol;Acc:621886]
Coordinates
chr3:58866731-58869061:+
Coord C1 exon
chr3:58866731-58866877
Coord A exon
chr3:58866878-58868945
Coord C2 exon
chr3:58868946-58869061
Length
2068 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
GGTATAATTTGTGTTTGCAGGAC
3' ss Score
7.17
Exon sequences
Seq C1 exon
GGTGTGGTCTGCACCCTGCATGAGGGAGATGACTTTGGCAAGTTAGCTCTGGTGAACGATGCTCCGAGAGCTGCATCCATTGTTCTTCGGGAAGATAATTGTCACTTCCTAAGAGTTGACAAGGAAGACTTCAATCGGATTCTGAGG
Seq A exon
GTGAGTTGAGAGAGTAAAGCTTGGTTGAAGAACATTCAATGTTTCCCCTTGTTGAAAAGAAAAAAGAGAGAGATTTGAGTAGATTGTTCATCCCACAGGAATGTGGCGAATAGATGCTTAAATGGCCTTTGTTATGAAAAAGGCATGTTTAGTGGACTGGTGTACATTCTGGAGACCAGCTGGAGACATCAGATATTATGCTGGAGCAAATACCTCTGCCTATGCTGGTCCCTATGACTGAACAACAATAGCACTTGCCTTAGCAAGATAGCACAGTCTAATAATGTATTTCTCACTGGTCTCCTACAGATCCTTCTTAATGTCCTTTTTGACCCTCCGATCCAGCAAAGTGGCAGCCTCCCTGTGCCCCCTGTCTTCTCTGTGGTCCATTTCCCACCTCTTCCCAAGTGAATCAGTCTTATAGTGTCACACACTCTGGATTTCCTGCGTGCTTGTTAATAGAAATTAATGCCTGTTGTGGTTATCCCACAAAGCGTATTCACTCATGGGGTTTACCGCAGGTCATTTCAAGCCACAGCTGTTACGGATATTGGCAAACAGGTGAATGATTTGGGTGGTCAAAGAGCAGCAGAATTGCACCTGAGGCTGGCTTCAGACGAAGAGCCTCTCTATAGCTGCTTAAGGTATCTGTAAGAGTGTGGGATGTTAAATCCCAGAGAAGATCCCTCTGGCCCTGCCCTCGCAAGCGAACTTCTTTCTCTATACTGCCTGAAGCCCTGGTCTCTTCTCGAAACACTGCTTACATGCTCAGTCACGACGCAAAGAAAGATAAAGTTCATACCACTGAGAAGGCTGGAAGTGTAGCTCAGCTGGTTGAAGGCTTGTCAGTATACCTGAAGCTCTGGGTTCAATCCCTAACACTATGAACCAGGCATGGTGGTGCACAGCTATGGTCATCTCAGCACTGAGAAGGTGGAAGCCTATAGGATCAGAAGTTCAAGCTCAGGCTCAGCTACGTAGAGAGTTTGAATAGCCTGGGGCATATGAGACCCTGTCAGTAATAATTATAATGATAGTAGTAATTATAAAATTTATACTGTTGACTAATATGGGGAAATGTATCATAGGAATTCGATGCTCAGTTGGTTTCATTTAAAATGGAGATCAAATATTCAGAAAAAGTAGTACAATTTTAAGAGTAAATAATTTAAAGTATTTTAAGGTAAACTTGACTAACTCTGAAGTTTACACCAAAAAAAAAAAAAAGGATTTGAACCACCACAGTTGAACCATTTTATCACTGACATTTAGAAAGCCATTCAAAATAACTGAGAAAGGCTTGGGACACATTTCAATTTGACTTTGAAAGAACTGTTACTTGGGGCTGGAGAGATGACTCGAAGTGTTTGCTCTGTAATCATGAGAGCTTGATTGACTTCAGATTCCCAGAACTCACCTAAAAAGCCAAGTACAGTGGTGTAACCCTGATGCTGGGACCTCGGAGACAGGGGGACCCATGGGGCTGGCTGAATTCTAGTTGAATCAGAGAACTCCAGGTTCACTGAGAGACTCAGTCTAAAGAGAATAAGGTGGAGCTTGGTTGAGGTGTAGGCCCCTGGCTTCTGCATGCAGGCTCACAGAAGAGGAGTGCACACAAAGAAACATGAACGTGGCTATATCCACACATGTCCAGGTTGAAACAAAACGGTTGCTCAATTAGACGGAGGTGCCACTCCTACGGATCATAGAAAAGGACTGATGAAACTCAGTATTGTCTGGTACATATTTTTAGAAAGAATAAATGCCTCCAGTTCACCCATTCTCTGCTCCATGCCCTCCCCCCAGAGGCTTTGCAGAGCGCCACCACCACACCAGACTCCTCTGGAGTTTTTCTGAGACTATGGTAAAAGCAGTTTTAAAAGCACATGCTTCAAACCTCATCTGGTCCTCCCTCTGACCGTTTCAGCCCTTGACTTTGAAAATGGCTTAATTTGTAGACGCGACAATTAACATCACAAGCGCCAAATGAGTTTCTGAAGCATTGGAAATTTCTGTCATTGTCTGAGTGAACGGCAGCATCTGTATGTGGTATAATTTGTGTTTGCAG
Seq C2 exon
GACGTTGAGGCGAATACAGTCAGACTTAAAGAACATGACCAAGATGTCTTGGTACTGGAGAAGGTCCCAGCAGGGAACAGAGCTTCTAATCAAGGAAACTCACAGCCTCAGCAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001516:ENSRNOT00000010630:18
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=0.385
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=FE(55.2=100)
A:
NA
C2:
PF0002724=cNMP_binding=PD(2.3=5.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
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]