DreINT0127034 @ danRer10
Intron Retention
Gene
ENSDARG00000062650 | rif1
Description
replication timing regulatory factor 1 [Source:ZFIN;Acc:ZDB-GENE-030131-3406]
Coordinates
chr9:22975889-22976213:+
Coord C1 exon
chr9:22975889-22976019
Coord A exon
chr9:22976020-22976121
Coord C2 exon
chr9:22976122-22976213
Length
102 bp
Sequences
Splice sites
5' ss Seq
ATGGTTTGT
5' ss Score
4.88
3' ss Seq
TATGCATGTTTGTATTACAGGCC
3' ss Score
8.81
Exon sequences
Seq C1 exon
CAAATATTTCAGAGAATATATTGTCTACGCTCTGCAATGTTGTGGTAAAGTCCAAAGAGAAGTTTACGTGCACTCGGGCATTGTGGGTCATTTCAAAACAGAATTTCCCTCCAGAGGTGGCATCCAAAATG
Seq A exon
GTTTGTTTGCTTAGTCTGCCGGGCATTCATTTAATCATTTTTCTTTGCTTCAATTATTTTGTTAGTGATTTTTTTTATTTAATATGCATGTTTGTATTACAG
Seq C2 exon
GCCCCAGAGATTCTCAAGAGCCTAGAAGCGATGCAGACCAGAGAGGTGCAGTCCATCCTCATTGACCACGAGTCACTCAATGTCATCATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062650:ENSDART00000143972:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF122313=Rif1_N=FE(12.4=100)
A:
NA
C2:
PF122313=Rif1_N=FE(8.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAGAATATATTGTCTACGCTCTGC
R:
TGATGACATTGAGTGACTCGTGG
Band lengths:
210-312
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]