DreINT0127036 @ danRer10
Intron Retention
Gene
ENSDARG00000062650 | rif1
Description
replication timing regulatory factor 1 [Source:ZFIN;Acc:ZDB-GENE-030131-3406]
Coordinates
chr9:22976297-22976669:+
Coord C1 exon
chr9:22976297-22976486
Coord A exon
chr9:22976487-22976576
Coord C2 exon
chr9:22976577-22976669
Length
90 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
TACTGCTATGAATCCTGTAGGTG
3' ss Score
5.51
Exon sequences
Seq C1 exon
GTTACTGGAGCAGGCCCCTGTTCCGATGGCTGTTGGTGCTGTTTGCTGGGCTAAACTTGTTATTCCTCTGGTGGTTCATTCGGCCAATAAAGTGCGTCTGCGAGCGGCAGCTGCCCTGGAGCTCGGCATGCCTCTTCTTCTGGAGAAACAGCAGGAAGTGGCAGCCATTGTTGAGCCAATGATGTCTTCT
Seq A exon
GTAAGTGATTATAATTGACGATAAGTTCTATGTTGTGCAATGTAAAGTATAAATAACCATCTTACTGCATTACTGCTATGAATCCTGTAG
Seq C2 exon
GTGCTCATCCCTGAAATGCAGAAGCTCTTTGCGTCTAAGAACGAGACAAACATGTTGAAACTCTGGCCTTTGTTTGTAAGACTTCTGGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062650:ENSDART00000143972:7
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:
PF122313=Rif1_N=FE(18.1=100)
A:
NA
C2:
PF122313=Rif1_N=FE(8.6=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:
TGCTGTTTGCTGGGCTAAACT
R:
TCTGCATTTCAGGGATGAGCAC
Band lengths:
176-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]