HsaINT0084992 @ hg19
Intron Retention
Gene
ENSG00000173120 | KDM2A
Description
lysine (K)-specific demethylase 2A [Source:HGNC Symbol;Acc:13606]
Coordinates
chr11:66886740-66888829:+
Coord C1 exon
chr11:66886740-66887520
Coord A exon
chr11:66887521-66888704
Coord C2 exon
chr11:66888705-66888829
Length
1184 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CTTATATCATTATTCTTTAGTGT
3' ss Score
6.83
Exon sequences
Seq C1 exon
GAGTCTGACGGGTTCAAAATGGCGGCGGCTGCTTCAGCGGCTCCTCCTGTGTGAGGGAAACAACACCCCTCCCCGGCAGCGGCGGCGGCGGCGGCGGCTCTCGGAGCACCTTCCCAGCGGCTGGGCCCGTGGCCGCTCTGTCTTTCCTGGGCAGGGGACGCTCCGGGAGGAGGGGCAACGCCAGGGGGCCCATCCCCCGGAATCCCTCTTCTGCGACTGGGGAGTAGCCGGGGGGCTCGTCCCGCAGCGCGGAGCCAGACCTGAGGGGGAGACGCGAGGGGAGCCAGGGCCCCCATCCCGGCGCGCCGCGCCGCTCCCGCCCTGTCCGCCCCCCGGGGCCGGGGCCCGCGTTCCGGGGGGCCGGGGCGGCGCGGGGAGCCTCGGGCCGGCCGGTCTCAGCTGATCGGCCGCTGCTCCCGCAGGCGACCAGCCCCTGCTGGCCGAGGGCACGGCGAGGAGGGCGCTCCCTGCGGCCGGGGCCGGCCCGGGGCTCGGGCCCGGGCTGCTGACCGCTGGCCTGGGGGAGGCGGGGGCGCCCCGGGCTCGGCGCCGAGGGGTCGCGCTCCTCTCTCCTGACGCCTCCGACTCCCGGTCTCCAAAGCCAGAAGAGAAGGTTTGATTCAGCAACTGTTTGCTCCCTTTTCCTGGTCGCTCTGACCCTCTCTGGATACTGGGTTGATCCACGGAAAAACCGAAGACGACGTTTGGGATTTAATTATTCCTCTCAGCTTTGGAATCTTTTACTTCTCACTTGGACAAGAACTCAAGAGCAGAATCTCCG
Seq A exon
GTGAGTTTCCCCCTCCCCCCCCTCATTTGGAAGTTTGGTTGACTGTGTTATCCAAAGACTGAATGCAAAGTTTCTATCTCTTTTTCCGATGGGTGAACCATTGAAACGCCTTTTCCTGGGGGAGCCCAGCGAGATTCGCCCTTTTTCCTCTCCGGCCCTGGCTGCTCCATGCCCAGGCGGTCGTCGCCCAGGGGGTGCAAGCACGGTTTCCCTCCCGACTTCGGGCCAGGGCTTCCTCCGGGAGGGCTCTGCCTCTAACTGCTCTGCAAACTGTGTCATCGGGTCCTCTGGTCTCGTAGCAGTTTTGAAAGGATGCTGTTAACGTGGCTGTAATGTAGTGACAAAAACGGGGGGAACCTGTGTTCTCAATGGAAGCCATTATCCACGAGAATATTTAGAAAAAAGAAAACCCTTTCTTGGTATTACGGATTGACCGTCGCGCCGGCCGGTCTTTTATTTAATTTTTGGACAAGATGTATTTTCCTTGTATCCTTAGATGCAATCGTTTATTTTATTACTTTATCCAAAAAGATCAGATGGAATTTTGGTCCTTGATTTGCACCTCTGAAATTTGTTTCAGAGTTGTGCACATCTTGTGTTGGGGTGGAGGGTAGATTTGGGAATGATAAGATCCGGGGAGTCTAGAAAGGAAGGCGACGATTGTGCACGGCCTTACAGGAGGGGTATGGGAAATTGTTTTGGGGTCATTTAAATCCTAATTTTTTGTCCTCTTTTTACATAGTCAGTTTGCCCTTCTTTCCTTTAGTTTCTGATTACCGGTGAGAGAGAACTAATTTGGTTAGGATCTGGATTAGTTCAGTGGTGCTTCACCTGGTCAGCTCTCTGGAGATAAAAGTCCTGGGCTTTTTTTTTTTCTTGCTGATGCTGCCATGAAGGAGATCCTTGCTAGTTGTAATCCTGTGGGGAGAAACTGGTGGTGTGGCCCTTCCACAAGGAACTGAAACCAACATCTCGTTTCGTCTAGGCCTCCGACAGTTGTAATGTGATTAATGTTGAACATGACATGGAACCACTTGCCCAAGAGCAGAAAGGTCCCAAACTCATGAAGAGGAACCTGATTTTTCAGAGAGCCTTTAACACTTACCTTAAATACTCCTTTCCGTGAACAGAAAGCACAAGTTTGAGAATGAGTTCTCATTTCTGCTTATATCATTATTCTTTAG
Seq C2 exon
TGTTGCAATCTGGTTCCTAAGGAGGAAGAGGAAGGCAGCCCTGGAGTGGTTTCTTTACAGTAATTTCAACAGAAGAGTGAGAGATGGAACCCGAAGAAGAAAGGATTCGTTACAGCCAGAGATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000173120-KDM2A:NM_012308:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.686
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCTCTCTCCTGACGCCTC
R:
ATCTCTGGCTGTAACGAATCCT
Band lengths:
342-1526
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)