HsaINT0085001 @ hg19
Intron Retention
Gene
ENSG00000173120 | KDM2A
Description
lysine (K)-specific demethylase 2A [Source:HGNC Symbol;Acc:13606]
Coordinates
chr11:67020924-67021889:+
Coord C1 exon
chr11:67020924-67021082
Coord A exon
chr11:67021083-67021673
Coord C2 exon
chr11:67021674-67021889
Length
591 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
CTCTTCTCTTGCCTGTACAGGTC
3' ss Score
11.77
Exon sequences
Seq C1 exon
GACTGAAAGACCTCCTCCTAGCAGGCTGCTCCTGGTCTGCAGTCTCTGCCCTCAGCACCTCCAGCTGCCCCCTTCTCAGGACCCTTGATCTTCGGTGGGCAGTAGGAATCAAGGACCCTCAAATTCGGGACTTGCTTACTCCACCGGCTGATAAACCAG
Seq A exon
GTATGCTCTGGACCTGACTTCTCTGTGCTTGTCTTGGGGTAGCTTTGTCTTCCAAACAGACCTCGTCTTCAGAAGCTAAGGTAGTCTCAGATATGACGCTGTGGAAGAATAGAAGAGCACAAAATGAAAACAGAATGATGGACTGTGTACAAGAATAGGGTAACTATAAGCAGATAACTACCTACAAACAATGGAGTAAGTCCATTTTGTGAGTTGGTGGAGTTTGGGGCCCAGAGAGTGTAAGCCTGAAAAAGTCTGAGAAGGCTTTATGGTGGAGGTGGAGTCAAAAGCTATTTGCATGATGGTCTAGAAAAGTGTGGTGGTATTGGAAGGGGAGGAGCATTCTGCACATAGCCTTTTGCTGTGTGCATGAGGCATAATCTAGCAGCTTGAGAAGAAAGAAAACTTGTCTGGTTTCCTAGAAACTGCCTACACCCAGTGCTCACACCCTGAAGGCATGGCTGGGTGTGGGCAGTTCTACTTAACCCCTTCAAGGGGGCCTGGCCAGCAAGTAGCTGTTGCTGCCTGGAGCCTTGAAGCTGGATTAGAGAATTGAGAGTTTTGATCTAGGCTCTTCTCTTGCCTGTACAG
Seq C2 exon
GTCAGGACAATCGCAGCAAGCTCCGGAACATGACCGACTTCCGGCTGGCAGGCCTTGACATCACAGATGCCACGCTTCGCCTCATAATTCGCCACATGCCCCTCCTGTCTCGACTCGACCTCAGTCACTGCAGCCACCTTACAGATCAGTCCTCCAATCTACTCACTGCTGTCGGGTCTTCCACTCGCTACTCTCTCACAGAGCTCAATATGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000173120-KDM2A:NM_012308:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.167 A=NA C2=0.082
Domain overlap (PFAM):
C1:
NO
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:
AAAGACCTCCTCCTAGCAGGC
R:
AGAGTAGCGAGTGGAAGACCC
Band lengths:
348-939
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)