RnoINT0127085 @ rn6
Intron Retention
Gene
ENSRNOG00000054901 | Rif1
Description
replication timing regulatory factor 1 [Source:RGD Symbol;Acc:1562474]
Coordinates
chr3:37638075-37642306:+
Coord C1 exon
chr3:37638075-37638971
Coord A exon
chr3:37638972-37642159
Coord C2 exon
chr3:37642160-37642306
Length
3188 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
AAACTATCCCGTACTTTCAGGTT
3' ss Score
8.39
Exon sequences
Seq C1 exon
AAAGAGTTGGACATCAGCAATGTAGGAAAGGCATGCAAAGTAATGGATGGGTCCAGTCCAGAGGGAGTTGAAAGTATAGAATCCAGTGTGAGAAAGGACACATTTGGAGCTGCTGTCTCTGAAAAGAGTACCCAAATGGATGTTTCTGTAGATGTGGCAACAGAGGAAGATAATAAAAAGGATGAGTGTGAAGCAGTCACAACTGAAGTGAATGCTGAAGGAGTAGCCACTGAGGACTTTAATTCAAGTATGGGTCTTTCTGATACTACCACACCTGTAAGTAAGGATGTTCAGGCTGAGCATCCAGCAAGTGGGGAACTAGAGGCGGGTAGCAATGAATCTGATTCAGGCTCATGTGAGGAAATGAACAAAGAAATGGAAAGTTACAAAGCACAAATGAACACTGAAATTGACAATGCCAGGGTAAAGGATATGGACATGATTGCCAGCACCTCTAAATCTGAAGAAGCACTGATTGGGAGACTTGATGTCAACACTGAGGGCTTTGTTAGCGACATTGAAATGAGTTCTGGAGAAGGAACTGGTAAATGCAAAACTGAAACAAACATTGAACTTAATAAATTAGATGAAATAAAATTAGGTGGTAATCAAACTACAGTGGGAAATGAAACTCTGCAGGAAGTTTGCTTTACTTCAGAGAAAGTGGAGGAATTACCACAGCCTCTGATACCCGAAGTGACTTCTGAACTTGGAGCAGAAAGCAATAATGTATCCCCTGTCAAGTTAGAGCTGGATCCTTCCTTTGGATCAGCAAGTGAAAGTCCTAGTGGTGTGCAGGCACGCTGTGTCTGGTCGCCTTTGGCTTCTCCATCCACAAGCATTTTAAAGAGAGCACTAAAAAGATCCCAAGAAGATGAGATCTCACCAATTAACAAG
Seq A exon
GTAGGAGGAATGGCACTGTAATGCATCTGATGTTTGCTTGAAACATGTGGTCTCTATGTGAAACATAGTAAAGGACAGGGTATTAGGATCCTGGCCACTCACCATGGAAAGGACCGGAGGGTTTCAGGTAGTCTTGCACCTCACACTCAAGAACTTGATGCAAATGTGCACATGGGACATAATGGGTAGCTCTCCTTTAGGATTTTCCTTTTCTATAATTTGTGGAACCAGATTTAAGAAGGCAGGCAACACTGATTGTTGTTGGTCAGAAGGCTTAGTTAGCACTTAATACATGTTTGGACTTAGTAATATAAAAAAGTTCTAAGGCAATTAAAATAATTTATAACTACCTCATTTTTTTCTTTCTCGTAATCGTAATCCCCCTTTTTCTGTTGTGGAGATTAAATCCAGAGGCCCAGACTTTCATTTTTTGAGATAGGTTAACTTAAGTGCATGCCACCAAATCGCTTCTCCCCTATCATATTTAGTTTCTGTTTCTTTTTTTTTTTTGGTTCTTTTTTTCGGAGCTGGGGACTGAACCCAGGGCCTTGCGCTTCGTAGGCAAGCGCTCTACCACTGAGCTAAATCCCCAACCCCTAGTTTCTGTTTCTTTTTGAGGTTGGGGGAATTCAGTGTACAATGTTGAGTATGTTTGCTCTATGGTACATACTTTGTCACTGAGAGATTCCCAGGTCTTAATGTCTATTTCTCTAGCACTGATCTATATACACATTTGAAGAGTTTGAGGAAAAAATGGATCATCTAGATAATTTACTTTAGCTTTTGTGCCTTTTGCTTACATAGGTTGCTGAATGAATAAGAAGACTGTAGCCTCTGCTTGACATAAAACATGCCCTCAGCTTAGCAAAACATGTCCTCAAAAGATGTCATATTGATCTTTTCAACTTAATCTTGAAATTAGTATCTGATACTATAGATCATATATGTAGAATATATTTGAACATATTTGTATGTTGTGATCAACAAGCATGTATGTTTTTTAATCTTTCTTGGGTGTGGGAACTTCTGTTTTCCATGCTGACCTTGAACTGTCATTTATGCCCCAGCTAGGGTTATAGTCTATTTCATAACCATTGGCTAACAAGTATAAGATCTATTTTTACTATTTTTAGTTACATGTATATGCATGAGTGTATTAGGATATGTGCACAGGAGTGCAGGTATCAAGTTATGGGCAGTTGTAAACTGCTTAATGTGGGTGCTAGGACTTTTGAAGTGTAGTATGTGCTTTTTTTTTTTCTTTTCCTTTTTTTTTGGTTTTTTGAGACAAGGTTTCTTTGTGTCCTGGCTGCTATGGATCTGTTCTGTAGATGGGGCTGACCTGCAACTCATTGCCTGCCTCTACCCTACCTTCACTTCCAGGCGTGCTGGGATTAAATGCTTGCACATAACTGCCCAGCTGCGGTGTGAACTCCTAACTGCTGGACTCTTCTCTCCACTTTTAGTTTTACAATCTGGAAATTCACATTCTGAGACTTCAGAGATGAAATCCTTTAGGAAAATAAACGGCTCTTGATTTTGTTTGTTAGCTTTTATTTTCATGACAAAGGGCTTCACTGTGCAACTCTGGCTCTCCTAGAGTTAACAACTTGGTAGCTATATGCTTTTTTTGTTTGTTTTAAAGTAAGCAGGTTTATTGTGAACTGCAAAGGGTAGTAAGGCAGTTACAAGATGACAGAATTCTGAATTCATCAGAAGGCTTATACAGCTTAACTAGCTATTACTACTGTACTACTGTTTGGTAGGAAATTAGATTTAGTGTGTTCCCACCCTCCTTTTAAAAGATAGGGCCTTGCTATGTAGTCCTGGCTATCCTGGAACCTGCAGAGACCCTCCTGCCTCTACCTCTTACTAATGCTGGAATTAGTTTTTTTTAAACTACTGGAGGCAGATTTAATGTCTATTCTAAATAAAATAGGATAACATTTCTGAAGCAGCTACTTACAGGTTACCCATTCTTAAGAATCAGTCCTAGTAGATATATGAGATCTCTATAGCTAATAGCTCAATGTGAACATATTGTAGACCTTTAGAAGAAGCCAAATTAGCCACAGTGAGGTTAAGCCACAGTATTTTTATTCTTGCCTTCAAAGAGTTCAGGGCAGGGACTCTGGAGATAGCTTGGGTGGTGTGGTGTGTTTGCAAGGTATGCATGAGGACTTGAGGTCCAATTTCTAGAAGTAAAAATCCCGGGCTGGGTGGCATGTGCTACTTACTAATCTCTGTCTTGGGGAGACAGATAACCATATTCCTGGGGTCTGCTGCTTAGTAAGCCTAGGCCAGTGAGAAGCATCATCACACAAAATAAGTTGTACAACACCTGAGCAATCACTCTGTCACCTCAAAGTTGTCCTCTGACTTCTACATGCATATATTCACAAGTTTACAACGATGATTAAGAAGATATACCAGAAACTAGTTGCTAGTATCTATTAATCTGTAAATATAGTTTATTGGTCAACTAAAATCAAATTATTTAGGATTTTTAAGAGATTTCGTTTTTATTGGTGTGTATGTTTGTGTATGCAAAAGCTCCTGGTGAGGTCAGAAGAATGTGTATCAGATCCCTTGGAGCTGAAGTTACAGACTTCTGTAGAACTGGCTTGGTAATGTTGGTGCTAGGATTTGAACTCTGGCTGATATGATTATGCAGTTGGTGCTTTTAATACCTAAGTTGTGTCTCTTGAGCTCTTGTTTTGTTCTTTGAGGCTGAGGTTTCACTATGTAGTTCCAGACTGACCTCAACTTGGTGTGGTCTTCTGCCTCAGTCTCCTGATTGCTGGGATCACTGTGGATTACTGCCACTCCTGTGCTTTGTTTTGTAGACAGAATCTCACTATGTATCCCTGACTGATCTGGAAATCTATACTGTTTAGACCAGGCTGACCTCAAACTCATAGACATCTACCTGCCTTTGCCTCTTGGGTACTGTGATTGAATGTGTGCACAGTCACACCCTGCATATTTATTTGTACATTGTTGATTTAAAGAGTCTGGTGACTATAGAAGTGGTGTAGTATGTAATTTGAATGGATTGCAATATTAGGCAGTATCTGAAAGATGGAACAGGTGTGCAGGAGGGTTCTAGTAAAATAAGTTTGGAAATACTTGGTTTTGCACAAACTCAAGGTGTTGTCTTCTTAATGAAAACTATCCCGTACTTTCAG
Seq C2 exon
GTTAGACGTGTCTCATTTGCAGATCCAATATACCAAGCAGGATTGGCAGATGACATTGATAGGCGCTGCTCTGTTGTTAGGTCTCATTCTTCAAATAGCTCTCCTGTAATAAAAAGTGTTAAAACTTCACCTACTTCACACTCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000054901:ENSRNOT00000090575:39
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.809 A=NA C2=0.367
Domain overlap (PFAM):
C1:
NO
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]