HsaINT0031556 @ hg19
Intron Retention
Gene
ENSG00000101224 | CDC25B
Description
cell division cycle 25 homolog B (S. pombe) [Source:HGNC Symbol;Acc:1726]
Coordinates
chr20:3781618-3782035:+
Coord C1 exon
chr20:3781618-3781740
Coord A exon
chr20:3781741-3781900
Coord C2 exon
chr20:3781901-3782035
Length
160 bp
Sequences
Splice sites
5' ss Seq
ATGGTACAT
5' ss Score
4.52
3' ss Seq
TCTGTCTGTCATGTGGACAGTGT
3' ss Score
6.3
Exon sequences
Seq C1 exon
GATGGATTTGTCTTCAAGATGCCATGGAAGCCCACACATCCCAGCTCCACCCATGCTCTGGCAGAGTGGGCCAGCCGCAGGGAAGCCTTTGCCCAGAGACCCAGCTCGGCCCCCGACCTGATG
Seq A exon
GTACATCCAGAGAGCGGATCCCTGGGAGGGGCCTGGGGAGGCAGCCTCGGAGAAGAGGAGGGTGGCCCTGAACCCCCAGGCACTGGGAACTTTTCCTCAGGAGGATGGGGGCGGGAACTATCTCCACCTCTAAGTCTGTGTCTGTCTGTCATGTGGACAG
Seq C2 exon
TGTCTCAGTCCTGACCGGAAGATGGAAGTGGAGGAGCTCAGCCCCCTGGCCCTAGGTCGCTTCTCTCTGACCCCTGCAGAGGGGGATACTGAGGAAGATGATGGATTTGTGGACATCCTAGAGAGTGACTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101224-CDC25B:NM_004358:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.680 A=NA C2=0.663
Domain overlap (PFAM):
C1:
PF066178=M-inducer_phosp=PD(0.1=0.0),PF066178=M-inducer_phosp=FE(20.9=100)
A:
NA
C2:
PF066178=M-inducer_phosp=FE(25.6=100),PF066178=M-inducer_phosp=PU(1.3=2.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCAAGATGCCATGGAAGCCC
R:
AAGTCACTCTCTAGGATGTCCACA
Band lengths:
242-402
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)