RnoINT0124253 @ rn6
Intron Retention
Gene
ENSRNOG00000001516 | Rapgef4
Description
Rap guanine nucleotide exchange factor 4 [Source:RGD Symbol;Acc:621886]
Coordinates
chr3:58864575-58866389:+
Coord C1 exon
chr3:58864575-58864635
Coord A exon
chr3:58864636-58866312
Coord C2 exon
chr3:58866313-58866389
Length
1677 bp
Sequences
Splice sites
5' ss Seq
TGTGTAAGT
5' ss Score
7.65
3' ss Seq
CTCCATCTTTTTGTGTCTAGTGT
3' ss Score
6.95
Exon sequences
Seq C1 exon
GTGAAACGGGAGTTAGCAGGTGTTCTCATTTTTGAGTCTCACGCCAAAGGAGGAACTGTGT
Seq A exon
GTAAGTGCGAGCCCTAATGAAGCACTCTGCTTGGCCACGCCCCATGCCGGTCATGGTCAATGCTATATGCTTCCTATTGGCTCCACTATGACCTGACAGTCATATCACTGTGGTGCGCAGGCATACACTCCCCAGTGAGGGGAGGGGGGTTGAGGGGATGGAACTGGGAGGGCTCTCCGGATAGGCAAGTGGGAGAGTTTAAAGTTCAAAGTCATCCATGGCTACACAGCAATTTTGAGACTCAGTCACTAAAAAGGGCTTTATTTACAAAAAACTAATTTCTCGAAACTTCCTGTTACTGTTCTGTTTGAAGTATTGTGTTTCCCGGTTTTCTTCACACTGCACCATGGACTCCAAGCCCAAGAGGATTTCTTTGCCTCAGAAACTCATTTAGTATCAGTCATCAGAGACTCACATAGTCAGTGGTACACTCATATGGGGCCTCTCTCTAGAATTCACCTTGTTCTTCAGTTCTGTGATCAGATCTGGAAACAAGAAATTCAGACATTAATAGATGCATGCAGCATCGCTGATGCCGATTTCCCACTAGTGTGGCTAGATAGAAACGGACACCAAACCCAGGGACACATAGAATACTTTGTTAATCCCCAGCAATTAAGCAAACCTCCAGGGGACATGTTTTAGGAATTTTTTATCTTCGTTAGGTACATTGTGATAGTTAAAAATAAATGAAAAATACAAGTTATAGGAGGAAAATGAACTTTAAACATTGTATCTCAAAATGTCTTTTTCCCCCCAGTCACTAAGAACACTATTTCTAACACTGATACCTCTGTCAGCAAGAAACCTATTTCTTTCTTTTCTCTCTCTCTTTCTCTCTCTCTCTCTCTTTCTTTCTTTCTTTCCTTCTTTCTTTCTTTCCTTCTTTCTTTCTTATTTTTGCCTTTTCAGGATCACTTTTTGTATAATTTTGATTCTTTGTCTCTTTAATTCTCCTTTATTTAATTCATTTTCATTAGTCTGTTCATTTGCTTCATTCAGATCACTAGTCCTTCCCACTGTACTGTAAGATATTTAAATGGATGGAGACAGATTATTAAAATACTTTATTTTTATCAAAACATGCCTGTTTGTTCTACAGTTTAAATACTTTCCAAACAATGAAACTGTCCTCCAGCTAGTTCCCCCTTTAGCCTGCTCTGCCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCCCCTCCTCGGCAGTGATTTATACCCTGAACATGTTGGTTCTTATTCTAACCAATTAAAAACGTATGCATAAGTACTTATTTATCAACAAGCAACAGCACTGATTTGCGTGTTTTCAAACTTCACATTGCTGGTCAGATCATCTTTAAAACCCATTTTCCACAGCACAATACTTTGTGAATTGTGAGGGAGACCTGCTTTCCATTAAGAAGAAGAGCATTGCTGGTAAATTGATACCCAGTAAGAACCTGTCTTTCAGGGCAAAGCAAATATTCCAGTCTCTTGTTCTTTTATGTGCTACAGAGAGACAATAATATTCTACCTGAATTAGTTAGGATCTGCCGGTAATTTTTTTTTTACTTTATGTATGCGTAATTCTGGAGCCTGAAAGTGATGATTTGATAAGCTGTAATTTATATTGATGTGCTTCTATTCTTGTCATAAGTCTCTCCATCTTTTTGTGTCTAG
Seq C2 exon
TGTTTAACCAGGGGGAAGAAGGTACCTCCTGGTACATCATTCTGAAAGGATCCGTGAATGTAGTCATTTATGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001516:ENSRNOT00000010630:16
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:
PF0002724=cNMP_binding=PU(10.3=42.9)
A:
NA
C2:
PF0002724=cNMP_binding=FE(28.7=100)
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]