HsaINT0085014 @ hg19
Intron Retention
Gene
ENSG00000089094 | KDM2B
Description
lysine (K)-specific demethylase 2B [Source:HGNC Symbol;Acc:13610]
Coordinates
chr12:122016707-122018920:-
Coord C1 exon
chr12:122018691-122018920
Coord A exon
chr12:122016852-122018690
Coord C2 exon
chr12:122016707-122016851
Length
1839 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
TCTGGTTTGGGTCCTCGCAGCGC
3' ss Score
7.02
Exon sequences
Seq C1 exon
GTGTGTCCACATCTTTGAGTGCCGGGAGTTTAAAAGTTAGGCAGTCCTTATAGGTATGGAAGCCGAGCTAATTTCCTTCTGAGCCCCCCAAATGCCTCCTCCACATGGCGGGTCCGCAAATGGGGGGATCTGCAGAGGATCACCCCCCACGAAAAAGACATGCAGCAGAAAAGCAAAAAAAGAAAACAGTTATATATACAAAATGCTTTGAATTTGAGTCGGCCACACAG
Seq A exon
GTAATGTTGGGGGAGGGGTGGATGAAAGAAGAGGAAGAGGGGTAGCCCTGGGCAATGAGGGCAGGAACGGAGGTGGGGGGTCGTTTTTGGGGGTGCCAGGCCCCGGGGGCTTTCACGCCAGCATGCTCGGCTTGCATTTCCGCGCCTCCCGCTGAGGCCAGCCGTGCAAATCTGCACCTCCCTCCCCGCCCCCTCCTCCTTCCCTCCCTCCCTGCCCCGCCATCTCCGGGATGCGCCCGCCGCCTGCAACTCGGCCCTCCAAAAGTCAGCTCTGCACACAACTCCCGGGCGGCGGCGGCGCCTGCGTGCAGAGGCGCACTCGTGACCCAACAACAAAACAGCGATGCCACGGCGCTAACGGCGCCCGGTGCCTCCCGGGCTCCCTCCCCGCCCCATACCTCCTCGGGCCGCCGCCCCCACCCCCCCAAGCCCGGGCCGAGAGCCCCCCCAAATAGCCCGGCCGCGGGCTCCGAGCGCGATCGGCAACAATGTTTACGTTCCGGGGATTATGACGTCGACGCCTCCCCCCCCCCACAACTGCTGAAAATGGTTTCCTAGGACTTTGCAAACGGATCTGCCTAAGTGTTGGTGCAAAACTTTGTAGATCTCGGCTCTGGCTTGCTTTATTTATTTATTTTTTGGTTTGTTTTCTTTGGTCTTCCCTCCTTCCCCCCTCGGCCAAAATGCAGGGGGCAGGAGTGTTGACAATTAATTGGTGAACTCTCCTAAAAAAATGGAGGCAGAGAAAGACTCTGGAAGAAGATTGGTGTGTAGCTTTTTTTTTTTTTTTTTTTTTCCAAATCTGTATCTGGCATATGATAGATCTTTTTTTTTTTTTTTTTGGTTGTTTCTCGCTGCCTTTTCTTTCCTTTTCTGTATTTTGCAAGAGGACCGGGAAAAAAATATAATAAATTGCATGCAAAAGGAAGCAAGCTGCTTACTCCTCCAGCCCCTTGTGAGGCTTAGAGTCTCAGACACTTAAGTGGGGAGGTGGTATCGGGGAAAGGCGTGGAGGGGGGCTGAGCGGGCTCGGGGTTCGCCCGGAATCTGGGGGGCTGAGGGGCCGGGCGCTGGGCGGTGGAGGGAGGAGGCAGGGGGATGCGGGGAGTGGTGGGGGAGTCTCCTTAGGAAGTGAGTGTGCGCGCGCGCTTGTGGGGAGATGAGGCAGCTGCTGGTGCGTTTTGGGGTCTCCGATCCGAGCTTTGTGGCGGGCCGTCTGCCTCTCCCCCTTCCAAGCCCCGATTCTCCTCCCCCCACCTCCTCTTCTTGCACTGGCGGGCGGGCGGCGGGGGCGGCTGGGGTCTCAGCCCTTCCATTTCAGCTTTCCAGCTTCCCCGGTAGCTCGGGGGCGGCTCCAGCTTTAGAAATGCCGCCGGCCCCCGGTTCCGGCTTCCCGGCTCTGCCGCCGCGGCCGCTGGGGCTGCTGTTACCGCCGAGCCGGGCGCCGCAGCGGCTCCTCCTGGGGCCTACATTTGCCCCGCCAGCCCGTGTCCGGAGCCCCCTTCGCGGGTTACATAACCAGGCTCCCGGCCGAGTGGGCGAAGCCCAGCACATTTCGGGGGCGGGGGGCAGGGGAGGGTCCCCAGATGTCCCTTCAGTGCTTCCGAAGACACCGGAGGGGAGTACCCCGCGTAGAGCGCAGCTGGACCCTCGGGGTGCGGGCCCCTCTCCTTGTCCTGCTTTTCAGCATCTTTGGCAATTGCGCAAAGTTGCTTGGGTTGCAATGGTGGGGTGCAGGGGGCGCTCGGCTGCTGCACCTGTTAGTGCTGGGCCCAGGTTGAGAGGCGACCTCCAGCCCCCACAATAATGTCCCGGGCTCTCTGGTTTGGGTCCTCGCAG
Seq C2 exon
CGCCCGATTGACCGCCAGCGATACGACGAGAACGAGGACTTGTCGGACGTGGAGGAGATCGTCAGCGTCCGCGGCTTCAGCCTGGAGGAGAAGCTTCGCAGCCAGCTGTACCAGGGGGACTTCGTGCACGCCATGGAGGGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000089094-KDM2B:NM_032590:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.571 A=NA C2=0.161
Domain overlap (PFAM):
C1:
PF136211=Cupin_8=PU(6.1=45.2)
A:
NA
C2:
PF136211=Cupin_8=PU(19.2=71.7)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTCCACATCTTTGAGTGCCG
R:
CACGAAGTCCCCCTGGTACA
Band lengths:
353-2192
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)