HsaINT0085020 @ hg19
Intron Retention
Gene
ENSG00000089094 | KDM2B
Description
lysine (K)-specific demethylase 2B [Source:HGNC Symbol;Acc:13610]
Coordinates
chr12:121881815-121882339:-
Coord C1 exon
chr12:121882253-121882339
Coord A exon
chr12:121882076-121882252
Coord C2 exon
chr12:121881815-121882075
Length
177 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
CTCTCTTTTTGGCCTACAAGCAA
3' ss Score
3.03
Exon sequences
Seq C1 exon
ATTAAGGAGTCAGAGGGTGTGGTCAACGACGAGCTTCCAAACTGCTGGGAGTGTCCGAAGTGTAACCACGCCGGCAAGACCGGGAAA
Seq A exon
GTGAGTGCCGGGCTCCAAGTCCCAGGGTCAGTCGGGAGAGGGGCGGGCCTGGGCCTGGCCGGGACCAGCCTGTCCCAGGAGTTTCAGGCAGGTGGGTTGCCGTCGGCCTGGGGAGGAGGAAGGGCAAGTCCAAAGGTATACAGTTGGTCTGTTCATTCTCTCTTTTTGGCCTACAAG
Seq C2 exon
CAAAAGCGTGGCCCTGGCTTTAAGTACGCCTCCAACCTGCCCGGCTCCCTGCTCAAGGAGCAGAAGATGAACCGGGACAACAAGGAAGGGCAGGAACCTGCCAAGCGGAGGAGTGAGTGTGAGGAGGCGCCCCGGCGCAGGTCGGATGAGCACTCGAAGAAGGTGCCGCCGGACGGCCTTCTGCGCAGAAAGTCTGACGACGTGCACCTGAGGAAGAAGCGGAAATACGAGAAGCCCCAGGAGCTGAGTGGACGCAAGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000089094-KDM2B:NM_032590:15
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.983
Domain overlap (PFAM):
C1:
PF0062824=PHD=PD(35.4=79.3),PF0030115=Rubredoxin=PD(60.0=93.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGGAGTCAGAGGGTGTGGTC
R:
CCTTCTTCGAGTGCTCATCCG
Band lengths:
247-424
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)