HsaINT0085010 @ hg19
Intron Retention
Gene
ENSG00000173120 | KDM2A
Description
lysine (K)-specific demethylase 2A [Source:HGNC Symbol;Acc:13606]
Coordinates
chr11:66985202-66986874:+
Coord C1 exon
chr11:66985202-66985355
Coord A exon
chr11:66985356-66986758
Coord C2 exon
chr11:66986759-66986874
Length
1403 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
CTCTGTTCCCCTTCTCCTAGGCT
3' ss Score
9.83
Exon sequences
Seq C1 exon
GTCTTCTGGCTCATCCCCCCTACAGCCCACAACCTGGAGCTGTACGAGAATTGGCTGCTGTCAGGGAAACAGGGAGACATCTTTCTGGGTGACCGGGTATCAGATTGTCAGCGCATTGAGCTCAAGCAGGGCTATACCTTCGTCATTCCCTCAG
Seq A exon
GTAAGCAAAATGGGAAGAGTGGGTTATTTAGCCATTTTTTTCCTTAATGAAAAAGAAATTGATGGATTACCACCAAGAATAGTTATGATGCTGGGCGTCTGCAGAAAACAACAGTGTTTCTTCCTGTCATTATGGAATAGATGCTGAGGTTTTGTTTGTTTTGTTTTCAGTTTGAAAAGGCAGTGGTTTTCCAATAAAGTATATGAGAATTGCCAGCAGAGGCTTTTCAGGTATACACGTTTGGGCTCTGCATTAGCCCTAGTAATTTAGAATCTCTATAGATAGGACCTGTTCTGCAGGTGATACACAATCTATGTTGAAGAACTGCCTACTATTCTAGGGAATGGCTGTGAAGGCTGGAGTGCTCAGTCAGGGATGTTTTTGATCAAGTCATTAAATCAAAGTAAGTGCTTATAAAGATCACAGATTTTGGAGTCACAGACCTCTATTAGGATTCTGACTATGCATTTACCTGCTAGATACTACGCTTAGAGCAAATATTTAAATCTGTGTCTCATTTTGTTATAAGGAATATAAATGAGAACACATGTAAACCAAGCTTATCCAACCTGCAGGCCACAGGCCTCATGCAGCCCAGGATGGCTTTGAATGTGGCCTAACACAAATTCATAAGCCTTCTTAAAACATTATGAGATTTTTTTTTTTGCAATTATTTAAGCTTGTCAGCTGTCATTAGTATTAGTATATTTTATTTTATTTATTTATTTATTTATTTTGAGATGGAGTCTTGCTCTGTAGCCTCAGGCTGGAGTGCAGTAGCGTGATCTTGGCTCACTGCAACCTCCACCTCCCAGGTCCCAGTTCAAGCAATTCTCCTGTCTCAGCCTCCCGAGTAGCTGGGATTACAGGTGTGCACCACCATGCCCAGCTAATTTTTGTATTTTTACTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCGTGATCCACCCGCCTCAGCCTCCCAGAGTGCTGGGATTATAGGCGTGAGCCCCCGCGCCAGGTCATGTTAGCGTATTTTATGTGTTGCCCAAGCAATTCTTCTTCCAGTGTGGCCCAGGGAAGCCAAAAGATTGGACACCCCTGAATTGTAAACTATCTTGTACAGAGCCTGGTTTATAGTTGGTGCTCCAGTAAACGTTTATTATGTGCTAAGCATTTGATGTGCATTTTCTCATTTAATGCTCATGAGCAACCATAAGAGGTATTATTTATCCTGGTTTTATAGAGGAAATTGAGGCTTTGAGAGATTAAGTAACTTGACAAACCACTAAGAAGCAGAATCAGAGTGAAGAGTGTGATCTAGGGGTCTTGTACTAGTTCTCTGAGAGAGACTTACTGTAATGTGTGTTTTCAGCCACTGCCCTCTGTTCCCCTTCTCCTAG
Seq C2 exon
GCTGGATTCATGCTGTGTATACTCCTACAGACACATTAGTGTTTGGGGGCAATTTTTTGCATAGCTTCAACATCCCTATGCAGTTAAAAATATACAACATTGAAGATCGGACACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000173120-KDM2A:NM_012308:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0237317=JmjC=FE(50.5=100)
A:
NA
C2:
PF0237317=JmjC=PD(17.8=46.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTTCTGGCTCATCCCCC
R:
CCGTGTCCGATCTTCAATGTTG
Band lengths:
270-1673
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)