RnoINT0142389 @ rn6
Intron Retention
Gene
ENSRNOG00000006731 | Spc25
Description
SPC25, NDC80 kinetochore complex component [Source:RGD Symbol;Acc:1307811]
Coordinates
chr3:55450446-55450768:-
Coord C1 exon
chr3:55450616-55450768
Coord A exon
chr3:55450512-55450615
Coord C2 exon
chr3:55450446-55450511
Length
104 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
TCTTGTAATCTGTCTTTCAGAAA
3' ss Score
9.65
Exon sequences
Seq C1 exon
CGTCTTAAAACAGAATGGGTGAAGACGAACTGGCAGCCTTCGAGAAAAGCATAAACGAATTTGGGGACAAGTTCCGGTACAGACTCAGTGATAATCGTAGCCAGGTGCTGGGACTTAAAGATGCCTTCAAGGACTCCATTAGAGCGCTTTCAG
Seq A exon
GTACTGCCTGCCCTTAACTCCTAACCTGCGGGTTTTGCTGGTCTTATTTATTGTCTACTGTTATTTCAGCGGGATTAAAACATATCTTGTAATCTGTCTTTCAG
Seq C2 exon
AAAAGCTGTCTTTGAAACTAAAGGAAGAAGAAAGGATGGCTGAGATGATTCTGGAATATAAAAATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006731:ENSRNOT00000008837:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF121283=DUF3584=PU(29.5=93.6),PF083176=Spc7=PU(20.2=87.2)
A:
NA
C2:
PF121283=DUF3584=FE(14.8=100),PF083176=Spc7=FE(10.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTCTTAAAACAGAATGGGTGAAGAC
R:
ATTCCAGAATCATCTCAGCCATCC
Band lengths:
210-314
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]