DreINT0127010 @ danRer10
Intron Retention
Gene
ENSDARG00000062650 | rif1
Description
replication timing regulatory factor 1 [Source:ZFIN;Acc:ZDB-GENE-030131-3406]
Coordinates
chr9:22979396-22980854:+
Coord C1 exon
chr9:22979396-22979496
Coord A exon
chr9:22979497-22980767
Coord C2 exon
chr9:22980768-22980854
Length
1271 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TCAAACACTGTTCATTGCAGCTT
3' ss Score
6.4
Exon sequences
Seq C1 exon
GAAATAAAAAGGAGCGACAGGGTTCAGAGGTCCTCACACTTTTCCTGCAGGCATTGCAGTCCATTTTGTCATCAGACGCTCTGCCTCCTGAACGTGCACTG
Seq A exon
GTAAGATAACATCAAGTGGTCCAACCGTTTTCTCAGAGATTAAAAAGCTGACAAAACATTGCTGTCACTCTGATACAAGTTTTATTTATGTAGAATTGCAGTGTTTGGGTGTTCTGTGTTGGTCTGAGATAATTAGTCTAACAAAATGTGTATATTCCATACAAGGTATGAAGCTGATCGGTCACTTCACGTGACTTGCAGCATTCATTTGACTGGGTGCGTCTGGAAGGCACAAGCCGTGCACCTCCATTTGAAATAACAAACTTGCGCAAATTCTAGAAAAGATTGGATATGTAAAAGGCCCCTAAAAGGCTGCTGTCAATTGTGATCTCCAGCAGTTTATCTTCTTGCACAGACATGGTCAAATCACCTGATTTGTTGACACATGGGTTGTGGATCTGTTCCTTGGCAGATTAAGGGTCCTTTTCCCCTTAGCAAAAAAAGTTTTCCAAAGATGTCTGTTTCTTACCCATTTCGTTGCTTGTAGGATAAATATGGGCGCTCAAGTGACCGAGATGCAAGCAAGAGAATATGGTCATTTTTCAAAAAACAAAAAACAAAAAAAAAGATCGTTAAGACTAAGATAATAAATAAAACAGAAATAATTATTTCTTGTGCAGCCTGGTACCAATTGATCAGCGAACCGATACCAGTCCACAGCCTGGTGGTTGAGGACTACTGGTCTAAATGTTCTAGAATGAATTCTTCAGGATCATGTGACACTGCTGATAAAGCATTGAGGAAAATATATATTTTAAAAAGGAAAATATACATTAGAAAACTACATACAAACTAGATTTTATTCTGTCACATTATTCTTTAGAATACGTTTCAGACCATTTAGACCAGGGATCACCAAACTTGTTCTTGAAGGCCTATTCTCTATTCATCTATCTGTAATGATGATATGATTTTGTTGTAATATGTTTTTGCAGTACATTATTACCACTGTCTGCATTCTTTAGTGATTAAGTCGGTCACACCACATTAAAAGCACAGTGCTACGCCCATGACAATTCATGCCATCTCTTTGTACAGGGATTTAAATGGCACCCTCAAGCCAATTGCACTGTCACCTCTTTAAAATACTAAAGTATAATTCAGCAGATTATTATATTATTCTGCTTAAAGAGAATTGTTAGATTTGTTGAGATTTTTAATTGTTAGAGTTTATTAATCAAACTATTTTTCTCTCTAATTTAAATACTAGTTTTTTGGTTTAGCTCTGCTGTCTGTGCACATTGTCATTGCTCAAACACTGTTCATTGCAG
Seq C2 exon
CTTCTGTTGGAAGCCACTGTAAAGGGAATACCTCAGAAGGTGCTTGGTTCTGCAGCTTATCAAGTGGCAAACATGGACGTGTTAAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062650:ENSDART00000143972:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.000
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:
AAAAGGAGCGACAGGGTTCAG
R:
GTTTAACACGTCCATGTTTGCCA
Band lengths:
182-1453
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]