RnoINT0124279 @ rn6
Intron Retention
Gene
ENSRNOG00000001516 | Rapgef4
Description
Rap guanine nucleotide exchange factor 4 [Source:RGD Symbol;Acc:621886]
Coordinates
chr3:58843237-58846638:+
Coord C1 exon
chr3:58843237-58843358
Coord A exon
chr3:58843359-58846630
Coord C2 exon
chr3:58846631-58846638
Length
3272 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
GCCTCCCATGATTCCTGCAGTGG
3' ss Score
5.05
Exon sequences
Seq C1 exon
ACAATGCTGTGTTGGGACTGAGCTGGTAGACTGGATGATACAGCAGACGTCCTGTGTTCACTCCCGGACTCAAGCTGTTGGCATGTGGCAAGTCTTGCTGGAAGATGGCGTCCTCAACCACG
Seq A exon
GTAAGATGAGCCGCAGGCTCTGGAGAATTCTCAAGAAACACGAAGCGTATTTCCCTGGGTAAAGCTATTGCTGAATTCCCGAATGGGCCAGCAAGAATTACGATCCCCTTAAAGAACCACCAAGCTAGCATCTTCATTTACTAATACAAATGCAGCGAGCGGATGCTATTGATTGCTAGGTTCCACGGTGTACCTTCCTAACTTCCGAGAACAAAGGAAAGGAAAATGAAATTGCAGCCGGAGTGCATCAGCTCCAATTATGTTTATTAGTTTGCATTCATGGTTCATTGATAGTGTGATTATGCTCCAAGCATTGCATAGCGGTCCTGATGCAGGGCCAGAGTGAGAGAGCAATGAAATGTGTGGCCGGGCTGATGACATGAGAGTGAGTAATGAATTCAGAAACCGCCTTTTAACTGTGCCACTGTCTGGGAGAGCCAATTTGTATACCGGCAGGATGACCATATTTAAAATCAGAGCTGCGCTCTGCAATTGCTGTCTCTAGTCACTGCAGCAGCTCCCGCCGAACAGAAGAGATATTCCGGGGGCTGGCGCACGCCTGTCACTGAACTGCTAATGCCACTTGTTTAAGACTACTTTTCTAAACATGAAAATATTCAAATCATCCATTTCACTCGCCGACACCTGGGAATGTGGGAATAATAATTTTGCTTGAGTTTCTCAGACTTTAATGTGCAAACCAATCACCTGGGGATCTCACTGAAATGCATATTCCAAGTTTGCAGGCCTGGGGTGGATTTCTAAGCATACTGGTTGGCAAACTGTACCCATATGTTGCTGCTGCTACCTCAGCTGCCATCCCTGTTTGGGGGATCTGGAAGGGTTCACCAGTGTTCTTTGTCTTTTGAATGAATTGACAATCCATGCTATAAAGGGACTAAATGGCATTCAGACATCTAGGAGAGTGGTTCTACCCTAGTTTGCCCTCTTTTTTCTAACGGAGACCTAGATCTTGCTATTGATCACTTGGTTAGTATGTGTGAGTTCCTGGGTTTGAGCCTCCAGCTTTGCCAAAAGAAAGGGATGAGTTTTTTGGAAATTGAAACTGCAAGAAAATGACCACAATTTCCTTCAAGGAGTCTGTGACCTAGAAGCATGGTCCAGTTGGCTCTGTTCATGTCACTAATTAATACTCTTCCAAGTTGGGTGAGAAGTATGTCTAATGGCATATAGAAAGAAAAGCCTAAGTTCTGACATCCCAAAGGAATGTCTCCTGTAACACTGTCAAAGAAGCATTCTCTGACAGGAGTTTACCAGTTTGGGACACATGCCCCACACTATAGAAAAGGCCACCAAGGCGCAGTATGGTCATTCCATAAAAGCTGGCAGGTGCTCAGCGGGAAGCCCAGGAAAGCAAAATCGCTTGGGTGGGTCCAAGCGGCTATGGCTGGAATGACTGCAGATGGCATGGCTTCACTCCTGGCTGCCCCGCCTGGGTGAGGTGGAGTCTGAAGGACTCAGACTCTCCGCTGTTCGACTGCACGGCTCTTTCAGCTCTTTCGCCGGACTCCTGCCCTGTATTCCTGGCAGCCTCCTATTTATATTTTCAGTTTTGACCCCAAACTCCACTTTTCCCTCATGTGAGTTTACACTGTAGATGTTTAGCAGCACGGCTCAGGATATCAACACTGAGCTCACATTAAATGACCTTTGGCCAACGACAAACAGAAACTGTCTGCTTCCTAGGTCATACTGAGGTAGCTCCTTTTCTCATAGTGCGAGACAAAAGTCTCCAGAAGCAAAGCTCGCATACCTGGTGTGCGTCATCCACCCTATCTCATCTACTCCATACCATCTATCCATCCATCCATCCATCCATCCATCCACCCATCCATCCATCCATTGTCCCCATCTATCCACCCACCCATCTACCACCCATTTCATCCACCCACCCAACCACCATCACGTATCCCACCCCTCCCCAGTCACCCATCTACCATCCACCACCCACCATCCACCCATTGCATGCATGCATGCATGCATGCATCATCCATCCATCCATCCCATTCCATCCATCCATTCCATCATCCATCCATCCATCCATCCATTCATCTACTCACCCACCTACCCTCCCATCCCTGTGAGGCAGCTGGAAACCCCTTGTCTGCCACCAGCGACCACAACCTGACATTGAGAACCTTGAGAGATTAGTTAGGCCAAAGAACAAAACAACTGTTCAAATCCTGTTAGATTCTAGGCATTCACCGATGCTCCAGGATATGCAAACATGGCTGCTCTCCTCTGCTCTCCCCACTCAGGGAGAACCTCTGAGTAAGGGTGGCTTTGGAATAGATCTGGAAGCCCCACATCCAGGCCTTATATTTTCATGCTGAAACAAACCCTCCCTCCACCGTACAACCAGTGCCAGGCAGCTACGGATGTCAGCTCTGAGCCCGGGGCTCAGCCGACACCTTTTATTATTGGGCCTCTGTAAGAACATTCATTTTATGTCTGCTATGTCCACTGGACACTTTCCAGAGAGAGCCATCTCTCAGACAGACTTCCCAGCTTTCTGCCCCTCGGACCAATTCAACAAAGCCTCTGAGTATAGCTTTATCTCCTTCCCCCAGGACTCTTTGCCTTCACTGGCCCAATACTCCAGGCTGCACGGGCTTTTAAAACAATGTCATTTTGTCACCCATGTCCCCTTTGTCCAAACTCTCTCTTGGGGCTGTAATCTCCCACACAGAGCATTTCAAAGGCTTGTCCTCATCCCAGCTGGTACTATCATCCTTAACTCTAGAACCATGGCTGTCAGCTCTTTCAGCCCAATACCCTCCTCTCAAACAAAATTTAATAGAAGAATCCAAAATATCAAATAGAAAAGCCAGAGCTTCATTGACCTAAGAGGAAGTAGGGTCCAAAGGACCTACCAGCCAATTTATGCTCTGTCTGCCCTGAAGATCATGGGAGGGTGGCTGAGGCACAAGAATTCCCTGGGGCTTTGGCAACTCAAATGAACGATGCCATCAGGAGCTACACTTTCTCTCTAGTCAGACTGCCTTCCTTTTTTCCTTGACTCATTCATCCACTGCCTGTCCTCCCTCATTGTTTCCTGGGTCAATCCCCTTTTTGCTAGTTCCTTGTTGTCATGGTCATCCAACCACATGCTCAATCTGCAGGTATGAGTCTGACTGAGATGGACTCCAAGGCATTTGGGATGTATGNNNNNNNNNNNNNNNNNNNNNNNNNGGAACTGGGGGACACAGCGTCGAGCCCATGCTGACCCTTGCCTCCCATGATTCCTGCAG
Seq C2 exon
TGGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001516:ENSRNOT00000010630:9
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:
PF0061016=DEP=FE(58.6=100)
A:
NA
C2:
PF0061016=DEP=FE(2.9=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]