RnoINT0127078 @ rn6
Intron Retention
Gene
ENSRNOG00000054901 | Rif1
Description
replication timing regulatory factor 1 [Source:RGD Symbol;Acc:1562474]
Coordinates
chr3:37602903-37603862:+
Coord C1 exon
chr3:37602903-37602999
Coord A exon
chr3:37603000-37603734
Coord C2 exon
chr3:37603735-37603862
Length
735 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
TTAAAATGCTTGTTTTTCAGAGA
3' ss Score
8.12
Exon sequences
Seq C1 exon
GCTCACATTTGCAGTCAGAGCTCAGAACTGAGTAGTGCTGCTCTACAAGCCTTGGGATTTTGTTTATATAATCCCAGAATTACCTCAGGATTATCAG
Seq A exon
GTAGGTACATGGACTAATGCTAGTCATATTTGTTGACTTTATAGTTGAATATAGTTAAAGTACTGTTGTCTGTGGATAAACTGTAGCCCTCCTTAAGACGTTAATTTGGAGCGTGTGCACCTATACTAAGTGCAGGAGTCATACCTACCATGTGGGTTCTGGGGATTGAAGTTAACTAGGCTTGATGGCAAGGGCCTTTACTGGCTCAGTCTTTTTAGTAGAACATAGTAAGTTGGAAGTTAATATTTATCTATCTGATTTATGATTGATGTGGTAGTCATACCCCTAAGGAACTGTTGAGATGAAGAGTTCTTATATAACACTAGTAAGTGTTAGTTTGGAAGTGGTAATTCGGTATAGAACCTGATGCTCTCCAAGTGCTAAGTAGTACTATTGTTCTGTAGTTGGTAGTTTGCAACTGTAAAAGACACCTACAAGATCACTGTTAGAGGGACTGAGGGGTAGGTAATAAAGATAGCATAAAGTAAGACTCCTTAGCATCCTCAGATGACTAGTTAATTGAGTTGTATAAGATAAAAAAAGTTTTCAGTCTGCTACTGTGTGTTTCTCCTTTGGTCAGGATTTTTATTTTGTCAAGAAGTGATACTGGTTAGCATCTCTAGGGTCTGTGATCATTATCTCCATCTGCTTTGTTACTTTTATGTTTCTAGTTGAGAATTTAAAGATTTAATTGAACTATACTATGTAAATGAAATTAAAATGCTTGTTTTTCAG
Seq C2 exon
AGACAAATATTCAAGAACTGCTATTAACCTTGAATGGTATCATTAAGAGTTCAGACAAAAATGTGTGTACCAGGGCACTGTGGGTAATATCCAAACAGACATTTCCTACTGAACTTGTTAGCAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000054901:ENSRNOT00000090575:3
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(8.8=100)
A:
NA
C2:
PF122313=Rif1_N=FE(11.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCACATTTGCAGTCAGAGC
R:
CATTTTGCTAACAAGTTCAGTAGGA
Band lengths:
225-960
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]