GgaINT0050209 @ galGal4
Intron Retention
Gene
ENSGALG00000012484 | RIF1
Description
replication timing regulatory factor 1 [Source:HGNC Symbol;Acc:HGNC:23207]
Coordinates
chr7:34667038-34670441:+
Coord C1 exon
chr7:34667038-34669812
Coord A exon
chr7:34669813-34670303
Coord C2 exon
chr7:34670304-34670441
Length
491 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
CTGCTTCTCTCTGACAACAGATT
3' ss Score
7.49
Exon sequences
Seq C1 exon
GAAGAAAATGGAAAGAGTGAAAGCTGTATTGCTGATTCAGATGGAAACACAGGGGACTGCAAAGTGGATAATCCTCTGGAGGATGTGAAAGAGAAGTCTGCTTATCACATAGAGAAGAATTCAAACAGCGAAGAAGAGTCGTCAAGGGGTGATAGAACTGGAATCATTGGAGAGGAGTCATCAGTTGGAGAGGCATTAGAAAAAAGTGGTACAGAAACAGCTTCAAAGGAGTCCTTAGTAGGGAATGAAAACACTTCAGCTATCAGCTGCAGTTCTACTTCAAGTGATGTGATCTGTGGAACGCCACAGCCTGCGAGCCGACGGCAATCTTTTATTACACTGGAGAAGTTTGATAGTTCAGAGAGCAGGCCCTTCAGCCCTTCAGCTTTAAACAGTGTGTCAGAGGTGTCTCAAAGTGCTCCTGTGCCGGATAAACAGGGAAATATAAACGTATGCAAGACTGGTCGTAAGCCAGGGAAGTCTGGGGAAGAGAGTAGAAAGTCTTCACAATCCGAGCAGATTTCTGCTGCAAAACGAAGGCTGACGCGCAGGCAGAGTAAAATGGAGCAGCAAGGAAATCAGCAGGCCAAGCTGGTAACTAACTCAGAACAAGAAAAAGGTGCTCAGGAGTCTTTCGTTTCCAATAGCGTGGAAAATAGTCCCGAATCACCTTGCTCAATGGAGGACACGGAGCGTGTTCTCACTGCTCAGCCCCAACCTGTCAGCTCTCCAGAACCAGACATCAAAAAAGCTGAAGCTGTAATGGCAGAAATAGAAAAGGTCCGGGCGTTTGAAATGGATTCTAAAGAAAATACACCCCCGAAGACGGCCGTGTCCTCCGAGCAGGTAATGGGTGATGGCAGTCAGGGCCCACATGCATCTCTTAGTCAGAAAACACTGAGACGTTCTTCGAGACGGCGGTCAGAAAATGCAGAGATGGCAGCAGGTAGTCAGGATAAGGAGGATGGCTACCAAAAAAAAGACAAACGTAAAGAAGATGAAAAAGCCCTGCAGAAGAAGGTGCCCCAGACTAAAGAGGATGCATCCCAGAAGCAGAAAGCAGTCTGTGGGAAAGCTTCAGAACATGCCATCAAAAAAGAAAGCAGCCTACCTGAGAGAAGTGCTGCAGAGGACTTGGGCTCAAAGGAGCCTCCTGCTGCAAAGGGAGCTGATGAGGAAGCAAACAGAAGTGCTGGGAAGCCAGAAGACACATTAAAGAGTGACTCGGAAGGTCAGGACTGTAGCTCAGATACAGTAAGTGAGAAGAAAAGGGAGCGGCCACGATACCACACCAGGAGGAGTTCACAAGGATTGCTTTCCAGCATAGAAAATGCAGAGGCTGATGGCTCTGAGACCAAGAAGGAAAGTTTAAAGAAAAAATCTGGAAAAACAAAAAATAAAAGTGATTCTCTTGAAGGTAAACGGAAGGATGTCCAGCCAGAAAGCCAAAGCCATGGGGTGTCTTCTCAAGTAGATGAAAGTAAGAATCTGTCGGGGATGAATGAAAGTGAATTAAGCAGTGAAGTCAGCACAGATGCAGCACTGATGTCTGCACCATCTGATGTGAAAAATCAAGTGCTGCTTGCAGGTGCTGATGAAGCTGAGGGGTCTGCCAGCTCAAGGACTTCTCCCAGTACTCAGAATGTGAGCGTGGAACAAAGCAAAGCTGGTGTGTTGCCAGAATCTTTCAGTGACCCACGTGTGTCTGATGAAGTTTTGAAAGGAGATGAAAATAAATGCATTGAAAAGCAAAGCTCTGTGGAACAGCATTCGAGTGTTCAGCCTGAGAACGTACAAGGAGCAAACACTTCAGGTAGTGACCTCTCCTCTTTGCAAATGCAGGACTGTCAGCACAAGAGAAGCAAAAGGGTGAGAAAAGCCAAGAGCTGCGACTGCTGCTCGAAAAGAGTGAAGCAGCAAACATCACTCAGTGAGTCAAAAAGTGAGGATCCTCGTGAGCTGATTGAGCCTCAGGCCACACCAGTGCAGATGGCTGTCAGTACAGCAGAGGTGTCTGGCAGCTCGAATCTGGAGGAGAGCTTGTCCATCACACCTTGTGCCATGAGCACACCGCTGCCTCCTGCTAAGGAGTCCGGTATGTTGAGCTTGGAAAGAGAGAGAACGGGTGAAGACAACCTGCAAGGAAATTCTGGTGTTATGAAGGAAGAGGCAGAGAATCCAGCACACACAGCAGGTGAAGTCAGTGATCCTGTAGTGGAAATAAAAGTGAAAGAAGAGGTTGATGGGAACGACAGAGCTGAGCAGTGTGTGTCTGTGTCTGAGTGTGCTTCGGATGAGCCCAGCGACAGCTCTGTGGCTGCAGGGGATCAAAGTGAAGAGAAGGCAGCTGTAGAAAAGGAAGAAGAAAGCCAGCATGGGGAAATGGAGGAGGTCCCTGAGGCTGATGGTAGCAAACCTGAGACAAAACAGATGGATGAGCTGGAAGGCAATCGGGACGGCAAGGAGGAAGCTGAGAACGCTCTGGAAGAAGTTTGCATTACTCCAGATAACGAGATGAGAGAGGAACTGCTGGAAGCTGAAATCACAGTGCCTGAGAATGTGGCTGTAGGCAACAAAGATGTAGTAGTAGAAAATAAGAGTGCGGATTCGCCTCAGAAGCCAGAAGGCCTGGATTCTTTCACCTCGGTCAATGGGAGCCCCAGCGGTGTGCAGGCACGCTGCACGTGGTCTCCTTCAGCTTCCCCATCCACCAGCATTTTGAAGAGAGGTGTAAAAAGGCACCACGAGGACGATTCCTTGTCACCTGCTAATAAG
Seq A exon
GTACTGTGCAATTTGTTCTGTGATACGGTTCCTTCTGTTCTAATGCAGCAGTAACACTGCCTGTAGTGCAGTGAGTTCCAAACATGTGCAGTTATCCCCTTAATTTTGTCACTTGTGAATGAAGGTACATTGAGGATAAGGACCTGTAGATATTTGTGTAGTGCACAGACATCAGCAGGCTCGTATTACTGGGAGCTTGGGAGGTTTGTTGTCAGAACAGCCCCAATGGCTGCTCTGCTCTGCTCTGCCTGCAGGAGTTGCAATGGAACGAATGCCACTGCAAAATCAGGATCTTACCAATGGATTTTTGGGGAACACAGTGTTTCCTTTGGCAGAAGCCGTTGTAATCGTGGCTTCAGCCCTTGGGTGAATGGTGTCGTTCAGGAATTTCAGTGACCTTATCCATTTCAAACAGTTGTTTTGTCACTTCAGGCTCCCTTCAGCACACTGTTGTGGTTCATGCTATAAAAACTGCTTCTCTCTGACAACAG
Seq C2 exon
ATTCGTCGGGTCTCTTTTGCCAATCCCATCTATCAGGAAGGACTGGCTGACGACATAGACAGGAGAAGTCCTGTCATTAGATCCCATTCTTCACCGTCTTCACGAAGTCTTAAAATCTTATCTAATATTCAGACTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012484:ENSGALT00000037786:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.976 A=NA C2=0.457
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAAGGAGGAAGCTGAGAAC
R:
ATTGGCAAAAGAGACCCGACG
Band lengths:
342-833
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]