HsaINT0084999 @ hg19
Intron Retention
Gene
ENSG00000173120 | KDM2A
Description
lysine (K)-specific demethylase 2A [Source:HGNC Symbol;Acc:13606]
Coordinates
chr11:67017557-67020328:+
Coord C1 exon
chr11:67017557-67018269
Coord A exon
chr11:67018270-67020164
Coord C2 exon
chr11:67020165-67020328
Length
1895 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
TCTCTTCCCTTCTATCACAGGTG
3' ss Score
11.15
Exon sequences
Seq C1 exon
AAGCGGAAAATGGAAGAGAGTGACGAAGAAGCTGTGCAAGCCAAAGTCCTGCGGCCCCTGCGGAGCTGCGATGAGCCTCTCACGCCCCCGCCTCATTCACCCACTTCCATGCTGCAGCTCATCCATGACCCGGTTTCCCCCCGGGGTATGGTGACTCGGTCATCCCCTGGGGCTGGCCCCAGCGACCACCACAGTGCCAGCCGCGATGAGCGCTTCAAACGGCGGCAGTTGCTGCGGCTGCAGGCCACAGAGCGCACCATGGTACGGGAAAAGGAGAACAATCCCAGCGGCAAAAAGGAGCTGTCTGAAGTTGAGAAAGCCAAGATCCGGGGATCGTACCTCACTGTCACGCTACAGAGGCCCACCAAAGAGCTCCACGGGACATCCATTGTGCCCAAGCTGCAGGCCATCACGGCCTCCTCTGCCAACCTTCGCCATTCCCCCCGTGTGCTAGTGCAGCACTGCCCAGCCCGAACCCCCCAGCGTGGGGATGAGGAGGGGCTGGGGGGAGAGGAGGAGGAAGAGGAGGAGGAGGAGGAGGAAGATGACAGTGCAGAGGAGGGGGGTGCAGCCAGGCTGAATGGCCGGGGCAGTTGGGCTCAGGATGGAGACGAAAGCTGGATGCAGCGGGAGGTCTGGATGTCTGTCTTCCGCTACCTCAGCCGCAGAGAACTTTGTGAATGTATGCGAGTGTGCAAGACGTGGTATAAATG
Seq A exon
GTGAGCAGGGATTCAGGGGGTCAGGAATTAGGGGTATGGGAGTAGGTGGCAGGTTTTCCATATGAGAACAGCATGCACCTTGGCATCTGAAAGCCTGTGGGGTCTTATGAGGAGTGAATTGACCCTTTTTCCCAAACTTTGGGTCCTGTTTAAAGATGTAGCCTGTTGTACCCGCAGATGTCATTAGGGAACTGGCCATTTGCCTCCTGGCCCTGCTCTATACTTTCCCATGTCTCATTGTTATGGGGAGGGAGACTGATTTGCGGGATAGATTTGTAGTCTGTGATAAAACTTGAGAGTCTTGCGGGCTGAAAATTTCCTCCTCAAGTCAGCTGAACTCATCACATGTTGGTTGAGAGCCTATGATGTTCTAGTCACTCTTCTGGTGCTGATAACACAGATAACCTCACTTAAGCCCCTGACTCAATTACCTCTCCATTCAGTGAGAGAAGTGGGCATGCTTTTCAAGATGAATTTGAAGGTGCTTAACATTTTTCTTCAGTTTTAATGCTCATCCCCCCAAACCTGGATCAGAATTCCCTCTTCCAGCAAGCAGAGTCCAGTTTTGAAGCTTCCTTAATGAGAGCTACCATTTCTTCTTAAGTTGGACAGACACTTGGGGGAAAAAATTGCTAGTGATGATGAACAAGGAGCTTCCCATTGGGCATTGTTGGTTTTTCCTTAAACTCTGGTATATATTTACTCTAGGATATATCCTTTTTATCTGGGTCACACACATCCTATTACAGTAGTGTGGTGTCCTGACCAATGGCATTCACTCAGGAACTTTTTAGAAATGTCAACTGTCAGGACCCTCATAGGCCTCTTAAATCAGAACCTCTTGGGTGGGCCCAGCAGTCTGCTTTAACAAGCGCTCCTCCAGGGGACTCTGATGCATGCTCGAGTTTAGAGCAGCAAAATCTGCTGTATTGTCAGCAGCTTGCTTCTGCCATAGAAGCTTCATGTGCCACTGGTAAAATTGTTTCAGTCTCTAAATAGACCCTATTCTTTGCAAACATGAGTTTATTTCCCAAATCTGAATTAATGTATAGTGTATCTAAATTCTCCTTAATATTTCTCTGTCTAGGGCTAATAGGACTGCTTGGCTCTACCTCTTGGTTTTCAGGGCAAGGCACATCAGATTCCCGTTATGTGCTGTCTCTCTTCCCCTGCCAACCAGGCTGGGGGGCAGGGGCTATAAAATATTAAATTGAAGCCAGCATGTTGTGGTTTGTGGCCTGTAGATTTGTAGACTGCAGTGGAAAGCCAGGCCTATCCCTTTCAGTTCTGGTCTGGCCTGGCTAGAAAATGTCAGGATAGCACTGAGGCAGAACTTGAGGGTGAGAGAGGACTCTGTAAGCCTGATAAAGAGCCTCTTTTGACCTGATACAGTAATGGGCTGAAGGCAGGGTGAATTGTGGATGTGCTGAGTAGCACCCTGCATTTCAGGCAGCTGCGAGTGATTGACAAGGGAGGGAACGGAGCAGGCCTTCTTAGCTTTAGACAGTAAGAAGTCTAGAAACTTCAAGAGGCTCCCTTATATACACTTCAGCAGGAACCATGCCATTTTAATACAGATGAAGGGGCTATAGACTGTTGCTTGCTATGGGTCCCTAACAACTGTTGTGTTCTCAAACACTCCAGAATAAATCAGGGTAAAGTGGTCAAGTTATATACTATCAACATGTAGGTTTGCAAAGCGTCTAGTTGTTGTAGAGTTCAAGGCAATTTTTTGCCTATTCTGTGAGGCAAAAAATGATAAGGTGTGATCCCTGTACACTTGTAGAAGAACGAGCCTCCAGGTACTCTGCTTTTCCCAGAAGCCATAAGCAGCCTGTGATGGGAGCTCCACTGATCAAGTTAATGAAGGCGAGTTCTCTTCCCTTCTATCACAG
Seq C2 exon
GTGCTGCGACAAGAGACTTTGGACAAAAATTGACTTGAGTAGGTGTAAGGCCATTGTGCCCCAGGCCCTCAGTGGCATCATCAAGAGGCAGCCAGTCAGCCTTGACCTCAGTTGGACCAACATCTCTAAAAAGCAACTGACATGGCTCGTCAATAGGCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000173120-KDM2A:NM_012308:17
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.772 A=NA C2=0.082
Domain overlap (PFAM):
C1:
PF0064628=F-box=PU(72.3=14.3)
A:
NA
C2:
PF0064628=F-box=PD(25.5=21.4)
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:
GACATCCATTGTGCCCAAGCT
R:
TCCAAAGTCTCTTGTCGCAGC
Band lengths:
356-2251
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)