HsaINT0085011 @ hg19
Intron Retention
Gene
ENSG00000089094 | KDM2B
Description
lysine (K)-specific demethylase 2B [Source:HGNC Symbol;Acc:13610]
Coordinates
chr12:122016707-122018364:-
Coord C1 exon
chr12:122017925-122018364
Coord A exon
chr12:122016852-122017924
Coord C2 exon
chr12:122016707-122016851
Length
1073 bp
Sequences
Splice sites
5' ss Seq
TTGGTGTGT
5' ss Score
3.29
3' ss Seq
TCTGGTTTGGGTCCTCGCAGCGC
3' ss Score
7.02
Exon sequences
Seq C1 exon
CCAACAACAAAACAGCGATGCCACGGCGCTAACGGCGCCCGGTGCCTCCCGGGCTCCCTCCCCGCCCCATACCTCCTCGGGCCGCCGCCCCCACCCCCCCAAGCCCGGGCCGAGAGCCCCCCCAAATAGCCCGGCCGCGGGCTCCGAGCGCGATCGGCAACAATGTTTACGTTCCGGGGATTATGACGTCGACGCCTCCCCCCCCCCACAACTGCTGAAAATGGTTTCCTAGGACTTTGCAAACGGATCTGCCTAAGTGTTGGTGCAAAACTTTGTAGATCTCGGCTCTGGCTTGCTTTATTTATTTATTTTTTGGTTTGTTTTCTTTGGTCTTCCCTCCTTCCCCCCTCGGCCAAAATGCAGGGGGCAGGAGTGTTGACAATTAATTGGTGAACTCTCCTAAAAAAATGGAGGCAGAGAAAGACTCTGGAAGAAGATTG
Seq A exon
GTGTGTAGCTTTTTTTTTTTTTTTTTTTTTCCAAATCTGTATCTGGCATATGATAGATCTTTTTTTTTTTTTTTTTGGTTGTTTCTCGCTGCCTTTTCTTTCCTTTTCTGTATTTTGCAAGAGGACCGGGAAAAAAATATAATAAATTGCATGCAAAAGGAAGCAAGCTGCTTACTCCTCCAGCCCCTTGTGAGGCTTAGAGTCTCAGACACTTAAGTGGGGAGGTGGTATCGGGGAAAGGCGTGGAGGGGGGCTGAGCGGGCTCGGGGTTCGCCCGGAATCTGGGGGGCTGAGGGGCCGGGCGCTGGGCGGTGGAGGGAGGAGGCAGGGGGATGCGGGGAGTGGTGGGGGAGTCTCCTTAGGAAGTGAGTGTGCGCGCGCGCTTGTGGGGAGATGAGGCAGCTGCTGGTGCGTTTTGGGGTCTCCGATCCGAGCTTTGTGGCGGGCCGTCTGCCTCTCCCCCTTCCAAGCCCCGATTCTCCTCCCCCCACCTCCTCTTCTTGCACTGGCGGGCGGGCGGCGGGGGCGGCTGGGGTCTCAGCCCTTCCATTTCAGCTTTCCAGCTTCCCCGGTAGCTCGGGGGCGGCTCCAGCTTTAGAAATGCCGCCGGCCCCCGGTTCCGGCTTCCCGGCTCTGCCGCCGCGGCCGCTGGGGCTGCTGTTACCGCCGAGCCGGGCGCCGCAGCGGCTCCTCCTGGGGCCTACATTTGCCCCGCCAGCCCGTGTCCGGAGCCCCCTTCGCGGGTTACATAACCAGGCTCCCGGCCGAGTGGGCGAAGCCCAGCACATTTCGGGGGCGGGGGGCAGGGGAGGGTCCCCAGATGTCCCTTCAGTGCTTCCGAAGACACCGGAGGGGAGTACCCCGCGTAGAGCGCAGCTGGACCCTCGGGGTGCGGGCCCCTCTCCTTGTCCTGCTTTTCAGCATCTTTGGCAATTGCGCAAAGTTGCTTGGGTTGCAATGGTGGGGTGCAGGGGGCGCTCGGCTGCTGCACCTGTTAGTGCTGGGCCCAGGTTGAGAGGCGACCTCCAGCCCCCACAATAATGTCCCGGGCTCTCTGGTTTGGGTCCTCGCAG
Seq C2 exon
CGCCCGATTGACCGCCAGCGATACGACGAGAACGAGGACTTGTCGGACGTGGAGGAGATCGTCAGCGTCCGCGGCTTCAGCCTGGAGGAGAAGCTTCGCAGCCAGCTGTACCAGGGGGACTTCGTGCACGCCATGGAGGGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000089094-KDM2B:NM_001005366:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.818 A=NA C2=0.161
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF136211=Cupin_8=PU(19.2=71.7)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATTATGACGTCGACGCCTCC
R:
AAGCTTCTCCTCCAGGCTGAA
Band lengths:
358-1431
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)