DreINT0127026 @ danRer10
Intron Retention
Gene
ENSDARG00000062650 | rif1
Description
replication timing regulatory factor 1 [Source:ZFIN;Acc:ZDB-GENE-030131-3406]
Coordinates
chr9:22975476-22975794:+
Coord C1 exon
chr9:22975476-22975554
Coord A exon
chr9:22975555-22975697
Coord C2 exon
chr9:22975698-22975794
Length
143 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
ATATATTTATTGTCTTTTAGGTT
3' ss Score
10.71
Exon sequences
Seq C1 exon
CCGACTTAATGGAGAAGAAGGACGCCAGTTTCTGCCTGTGGTTGTTAAGCATTTTGCACGTCTTAGTAAAGTGCTTTTG
Seq A exon
GTAAGTTTGTCATATCTATAAGTAAAAAAAAAACTTCACTGAAGTCAATTGTATACGAATAAATGACTTTTCGTCTAAGACCAATCAATTATTTCAGATAACTTGGTCTATCCCTGCAGTTGAATATATTTATTGTCTTTTAG
Seq C2 exon
GTTCACATCTCCAGTGAGAATGAGGAGCTGTGTCAGGCTGCACTGCAGGCTTTGGGATTCTGTGTCTTCCACTCACACATAGTTTCAGTCATACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062650:ENSDART00000143972:3
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(6.6=100)
A:
NA
C2:
PF122313=Rif1_N=FE(9.2=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:
CCGACTTAATGGAGAAGAAGGACG
R:
TGACTGAAACTATGTGTGAGTGGA
Band lengths:
170-313
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]