DreINT0127027 @ danRer10
Intron Retention
Gene
ENSDARG00000062650 | rif1
Description
replication timing regulatory factor 1 [Source:ZFIN;Acc:ZDB-GENE-030131-3406]
Coordinates
chr9:22986140-22989305:+
Coord C1 exon
chr9:22986140-22989070
Coord A exon
chr9:22989071-22989182
Coord C2 exon
chr9:22989183-22989305
Length
112 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
TACATTTTTGTTGTGTGCAGTCA
3' ss Score
7.26
Exon sequences
Seq C1 exon
GAGGTTGCCTCAAATGAAGTACCAACCACAGATGTTAAAGTCCAAAAAGTCACCAGTTCTGATATAGAAACTCCAGATAAAGCTACGCCGAATAAAGATCAAACTTTGGAGATGGATCAATCACCATCTACTGGTGTCTCAGTTGATGTGAGTGGGCTTGAGAAAAGCGCATTGGAGGGGACAAGTCCTAATATTTCAAGTTCATCTGATGTGGTATCTGGCACACCTCCTAAACCTAACAGCAGGCGTCAGTCATTTATAACCTTAGAAAAATATGCTGAAGGGAAATCGACAAGTCCTGCAAGTCCTGCATTTACAGGTACGCTCACCCGGAGATCAAGAAGACTGGAGGCTTCACAGGCATCAACATCAAATCAAAATGATTCTCAACCTCAGATTAAAAAAGTGGATTCTCAGGAATCTCAAAAGATGAGCAGCATTGACATGTCCATTCAAAATGAGCATGCTAGCATGGAAGTAAAAGATGAGAAGTCAGTGGGAGCTAATCCATGTGAAGGTACAGATGAGGAAGATGTTGTTCCAGATACCCAAACCCAAGTATCTGGTGACACATTGGGTATTAAAAGCAGTCCTGTGTCTAAAGCCCATGCGGAGGCACAGGGGACTCCTGAAAAAAATTCACAGAGTCCTAATGATTCTCTAGCTAGTCAAGAACCAAGAAGGTCTGGCAGAAGGCGAAGTAAACCTGTTCGTCCAGGGCAAGATGCAGAGGAAATAAAAAGTAAATCTCAAGAACAAGCCAGTCAACCTGCAGACTCTGCGATAATAAACTCACAAAAGCCCCTTCTTGCTTCACCTAGTAGTACTTTGACTGGAAGAAGGAAAAAAAAGGTTGAGACCAATAAAATGGAAGACCAGCTGAACAATGAAGAAATGAAAGGAGATCTCAGCCAAAGCGATTCACAGATTTCCGCTGCTGACCCTCCACAGACAGTAGGTGTGCATGCCAATAAAGACTTAAGCCAGACTGAGTTATCTCCGAAGAGTTCTCCTGTAACCCAGTCAAATAGCCAAAGCAAAGAGAGACTGCCAGCTCTCTGCGAGTCTGAGAGTATGTCGTTAGGTAGACAGGAGACAAAAACACAACTTGAAGAATCCACAGAAAAGGAGACAAATAATGACTCTCAAAACGCTTCATCTGCAGCGAGACCGAAGCATATACAGTCTACCACGTCTGACTCCGAGTCGGATAGCCAGCAAATTGTCCGTAAACGAAGATCGAGGAGATCTGAAACTAAGTTACTGGAGATATCTGGTGTGCCGATCAAAGAAGACTTGAATCAGACAGACTCCCAAACTCCAACAGGAGTGAAGGGAAGAGCTATGAGGAGGAGAACCGTAGAAGGTGCAGAGTCTAGTAAAGATTCCACATCAGCGGTAAATACAGAGGAGTTAAGTGCAGGCAAGGAGTCATCACAAGAGCTTGGTAGATACAGAACTCGACGTTCTAGGGGTTTGTTGTCTCCTGAGAGTATGGAGTCTGAAAACTCTGATAGCCGAGAAGATGGGGCAAGGCCTAAAAAGAGGCTGCGAAAACCACCATCAACAGAGGTGTTACCTGTTGCTTCAGAACCCAAAGTTATTGAGATGGTACCAGAAAAGGACGATGTTCAGTCAGAGGTTTTAATGGAGACGTCAAAGGATGAGGCAGATCCTGAAAATATCTCGAATACTTCAGTCAGTGAAACCAAAGAACTTGAGCAAAAGAATAAAGAGGAAGTCCCTGCCCCTTGTGATGCACCACATGAACAGATTATCACGGAAAAAGCAGCATCAAACAACAAAATTGACACTGACTTAACTGATACAGACGAAAAAGAAACCGTCAAGGCAGAGGGTGAAGAAGCTAATGAATCTTCGCAAACTGGATCAGAAGATTTTAAAAAGACAGATGTTTTGCATAAATGCCCACATACAAAGGGACGGGGCCGTGCACGTAGACGATCTAAAAACTGCAACTGCTTTTCCAACAACCGTGATGTGTTTTCACAGGACAGTGACTTCCAAGAATCACAAGATCTAAAAAATGAACAGGTTCCACTTGCTGCCAACATCTTGAACTCTCAACCTGATCAGTCAAGCCCATCAACTGCATCAGAAGAAAACAAAAGCTCAGCAATTGAAGAAGTCCCTGTTGCGGATGTTCCATCACTTTCAGCCTTATCAGCTGATCTCCCATCTGAGGTTTCACCTTCTGAAAGTCCCATTACAAAACTTGGGGTAATTGTTTCTCAGCTACCAGAAGTGGAGAAAGAAGCACAGCCTGGATCATCCAAACCAATGAAGGATTCGAGCAAGGAGCTTGTAGAAGAAGTGAATCGATTAAGTTCTGGATCCACAGGTGGTCAAAAGCACAAAGGAGAAAATAGATTAGAAAACACTTCAGTAAGCCAAGAACCTGTCCAGAGTTCAACACCTCAAGACACGTCTCCAAGTCAAGGTCGTCCAGTGGACGATGCACCAATATGCCAGGAGCAGTTAGAGTCTTCTCATGTCCAGCAGGAAGATGCAGTTAACCCAGCAGTGATGGAAAGAGAAGACCTTGCTGTGTCAGAGCAGAGACAAGAGAAGGCTGTGTTGTCTGAAGAGTTAGATGGAAAAGGTTTGCTTGACAAGGAAACTACTCTTGTTGAAAAGGAAGAAGAGATGCAGGTTAATAACCAGGATCTTCCTGTGGATGTCCAAGAAGAGTTACCTGTAGTGTCCCAGAGTAGCACATCTGAAGCCTGCTTGGATTCTCCACCCAAGCCAAAACTGTTAAGCGCACTCAGTGGTGAACTAGAGCCTGGCCAGAGTCCAACTAGAAGTCGGTCTCGAGTCTGGTCACCATCTGCTTCTCCGTCTACCAGTATTCTGAAGAAGGGTCAGAAGAGAGCATGTGAAGAGGAGACTCCATCCCCCATTCCCAAG
Seq A exon
GTAATGACAGCATAAGTTACCATGCATCCATTAATGCATATGTTATTTTACAGCTTAATTTACTTTTGCATAAGTATTTTGACTATATATTTTACATTTTTGTTGTGTGCAG
Seq C2 exon
TCACGTCGAGTGTCTTTTGCAACTCCAATTTACCAGCAAGAACTGGCTGATGACATTGATCGTCGTAGTCCGGTTATTCGCACAAGTTCACCTAGGTCAAAAGTCTTGAGTGGACAGTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062650:ENSDART00000143972:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.989 A=NA C2=0.805
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGTTAAGCGCACTCAGTGGT
R:
TGACCTAGGTGAACTTGTGCG
Band lengths:
255-367
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]