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Gene: HMGN2P46 (high mobility group nucleosomal binding domain 2 pseudogene 46) Homo sapiens

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Symbol:

HMGN2P46

Name:

high mobility group nucleosomal binding domain 2 pseudogene 46

RGD ID:

1351115

HGNC Page

HGNC:26817

Description:

Predicted to enable chromatin binding activity. Predicted to be involved in chromatin organization. Predicted to be active in nucleus.

Type:

pseudo (Ensembl: transcribed_processed_pseudogene)

RefSeq Status:

VALIDATED

Previously known as:

C15orf21; D-PCa-2; FLJ39426

Related Functional Gene:

HMGN2

Latest Assembly:

GRCh38 - Human Genome Assembly GRCh38

Position:

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	15	45,511,136 - 45,556,730 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	15	45,555,482 - 45,555,971 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	15	45,803,334 - 45,848,928 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	43,590,626 - 43,636,220 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	15	43,590,625 - 43,636,220	NCBI
Celera	15	22,694,488 - 22,740,083 (+)	NCBI		Celera
Cytogenetic Map	15	q21.1	NCBI
HuRef	15	22,626,368 - 22,671,536 (+)	NCBI		HuRef
CHM1_1	15	45,921,545 - 45,967,131 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	15	43,319,297 - 43,364,888 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
HMGN2P46	Human	antirheumatic drug	decreases expression	EXP		6480464	Antirheumatic Agents results in decreased expression of HMGN2P46 mRNA	CTD	PMID:24449571
HMGN2P46	Human	cadmium atom	decreases expression	EXP		6480464	Cadmium results in decreased expression of HMGN2P46 mRNA	CTD	PMID:24376830
HMGN2P46	Human	copper(II) sulfate	decreases expression	EXP		6480464	Copper Sulfate results in decreased expression of HMGN2P46 mRNA	CTD	PMID:19549813
HMGN2P46	Human	fulvestrant	increases methylation	EXP		6480464	Fulvestrant results in increased methylation of HMGN2P46 gene	CTD	PMID:31601247
HMGN2P46	Human	hydrogen peroxide	affects expression	EXP		6480464	Hydrogen Peroxide affects the expression of HMGN2P46 mRNA	CTD	PMID:20044591
HMGN2P46	Human	lipopolysaccharide	increases expression	EXP		6480464	Lipopolysaccharides results in increased expression of HMGN2P46 mRNA	CTD	PMID:35811015
HMGN2P46	Human	lipopolysaccharide	multiple interactions	EXP		6480464	[S-(1,2-dichlorovinyl)cysteine affects the susceptibility to Lipopolysaccharides] which results in increased expression of HMGN2P46 mRNA; [S-(1,2-dichlorovinyl)cysteine more ...	CTD	PMID:35811015
HMGN2P46	Human	S-(1,2-dichlorovinyl)-L-cysteine	multiple interactions	EXP		6480464	[S-(1,2-dichlorovinyl)cysteine affects the susceptibility to Lipopolysaccharides] which results in increased expression of HMGN2P46 mRNA; [S-(1,2-dichlorovinyl)cysteine more ...	CTD	PMID:35811015
HMGN2P46	Human	sodium arsenite	decreases expression	EXP		6480464	sodium arsenite results in decreased expression of HMGN2P46 mRNA	CTD	PMID:34032870

Biological Process

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
HMGN2P46	Human	chromatin organization	involved_in	IBA	MGI:96120\|PANTHER:PTN000557317	150520179		GO_Central	GO_REF:0000033

Cellular Component

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
HMGN2P46	Human	nucleus	is_active_in	IBA	MGI:2138069\|MGI:96120\|MGI:96136\|PANTHER:PTN000557317\|UniProtKB:P05114\|UniProtKB:P05204\|UniProtKB:Q15651	150520179		GO_Central	GO_REF:0000033

Molecular Function

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
HMGN2P46	Human	chromatin binding	enables	IBA	MGI:2138069\|MGI:96120\|PANTHER:PTN000557317	150520179		GO_Central	GO_REF:0000033

#	Reference Title	Reference Citation
1.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

PMID:12477932	PMID:12727900	PMID:14702039	PMID:15027122	PMID:19322201	PMID:24043589

Variants in HMGN2P46
14 total Variants

Predicted Target Of

	Summary Value
Count of predictions:	1086
Count of miRNA genes:	525
Interacting mature miRNAs:	557
Transcripts:	ENST00000313559, ENST00000396644, ENST00000396645, ENST00000409454, ENST00000495658, ENST00000564594, ENST00000568669, ENST00000598619
Prediction methods:	Microtar, Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2289410	BW327_H	Body weight QTL 327 (human)	3.32	0.0001	Body fat amount		15	19980129	45980129	Human
1643273	BW330_H	Body Weight QTL 330 (human)	1.05	0.014	Body weight	body mass index	15	26866719	52866719	Human
2289430	BMD7_H	Bone mineral density QTL 7 (human)	3.32	0.0001	Bone mineral density		15	19980129	45980129	Human
1559411	SCL107_H	Serum cholesterol level QTL 107 (human)	3.88		Lipid level	triglyceride	15	26543552	52543552	Human
2299958	PRSTS330_H	Prostate tumor susceptibility QTL 330 (human)	1.02	0.0151	Prostate tumor susceptibility		15	34790230	60790230	Human
1643523	BW284_H	Body Weight QTL 284 (human)	1.95	0.0013	Body weight		15	21792889	47792889	Human
1559354	LDLPS4_H	Low density lipoprotein particle size QTL 4 (human)	2.2	0.019	LDL particle size		15	34790230	60790230	Human
2289420	BW314_H	Body weight QTL 314 (human)	2.72	0.0003	Body weight	lean mass	15	19980129	45980129	Human

D5S1597E

Human Assembly	Chr	Position (strand)	Source
Cytogenetic Map	3	p25.3	UniSTS
Cytogenetic Map	17	p11.2	UniSTS
Cytogenetic Map	16	q24	UniSTS
Cytogenetic Map	20	q11.22	UniSTS
Cytogenetic Map	22	q13.1	UniSTS
Cytogenetic Map	12	q13.13	UniSTS
Cytogenetic Map	19	q13.4	UniSTS
Cytogenetic Map	10	q23-q24	UniSTS
Cytogenetic Map	1	q25.1	UniSTS
Cytogenetic Map	14	q24.2	UniSTS
Cytogenetic Map	9	q34.11	UniSTS
Cytogenetic Map	14	q11.2	UniSTS
Cytogenetic Map	12	q14.3	UniSTS
Cytogenetic Map	8	q24.11	UniSTS
Cytogenetic Map	16	p13.3	UniSTS
Cytogenetic Map	19	p13	UniSTS
Cytogenetic Map	18	q11.2	UniSTS
Cytogenetic Map	6	p22.1	UniSTS
Cytogenetic Map	14	q32.12	UniSTS
Cytogenetic Map	10	p13	UniSTS
Cytogenetic Map	15	q22.2	UniSTS
Cytogenetic Map	1	p22.1	UniSTS
Cytogenetic Map	19	q13.31	UniSTS
Cytogenetic Map	7	q22	UniSTS
Cytogenetic Map	19	q13.3	UniSTS
Cytogenetic Map	19	p12	UniSTS
Cytogenetic Map	1	q41	UniSTS
Cytogenetic Map	3	q23	UniSTS
Cytogenetic Map	17	q21.31	UniSTS
Cytogenetic Map	17	q21	UniSTS
Cytogenetic Map	20	q13	UniSTS
Cytogenetic Map	5	q13.2	UniSTS
Cytogenetic Map	1	p35.1	UniSTS
Cytogenetic Map	21	q22.13	UniSTS
Cytogenetic Map	22	q13.2	UniSTS
Cytogenetic Map	7	q11.23	UniSTS
Cytogenetic Map	7	q21-q22	UniSTS
Cytogenetic Map	17	q25.3	UniSTS
Cytogenetic Map	18	q12.2	UniSTS
Cytogenetic Map	7	q36.3	UniSTS
Cytogenetic Map	1	p36.13	UniSTS
Cytogenetic Map	12	q24.31-q24.32	UniSTS
Cytogenetic Map	12	p13.3	UniSTS
Cytogenetic Map	1	q21.2	UniSTS
Cytogenetic Map	X	p11	UniSTS
Cytogenetic Map	1	q21.3	UniSTS
Cytogenetic Map	14	q32.31	UniSTS
Cytogenetic Map	17	q22	UniSTS
Cytogenetic Map	1	q42.12	UniSTS
Cytogenetic Map	22	q13	UniSTS
Cytogenetic Map	11	q24.2	UniSTS
Cytogenetic Map	13	q33.3	UniSTS
Cytogenetic Map	7	p14.3	UniSTS
Cytogenetic Map	20	q13.1	UniSTS
Cytogenetic Map	1	p31.3	UniSTS
Cytogenetic Map	X	p22.11	UniSTS
Cytogenetic Map	20	q12-q13.12	UniSTS
Cytogenetic Map	3	p21.31	UniSTS
Cytogenetic Map	12	p13.31	UniSTS
Cytogenetic Map	7	q31	UniSTS
Cytogenetic Map	X	q13.1	UniSTS
Cytogenetic Map	11	p11.11	UniSTS
Cytogenetic Map	16	p13.11	UniSTS
Cytogenetic Map	21	q22.3	UniSTS
Cytogenetic Map	6	p21.3	UniSTS
Cytogenetic Map	17	q25.1	UniSTS
Cytogenetic Map	10	q11.21	UniSTS
Cytogenetic Map	3	q28	UniSTS
Cytogenetic Map	11	p15.1	UniSTS
Cytogenetic Map	11	q24	UniSTS
Cytogenetic Map	16	p11.2	UniSTS
Cytogenetic Map	8	p11.2	UniSTS
Cytogenetic Map	X	p22.31	UniSTS
Cytogenetic Map	17	q23.2	UniSTS
Cytogenetic Map	4	q13	UniSTS
Cytogenetic Map	4	q35.2	UniSTS
Cytogenetic Map	22	q13.33	UniSTS
Cytogenetic Map	15	q21.1	UniSTS
Cytogenetic Map	14	q32.33	UniSTS
Cytogenetic Map	20	p13	UniSTS
Cytogenetic Map	2	p12-p11.2	UniSTS
Cytogenetic Map	7	q22.1	UniSTS
Cytogenetic Map	14	q12	UniSTS
Cytogenetic Map	12	q13.12	UniSTS
Cytogenetic Map	5	q12.1	UniSTS
Cytogenetic Map	15	q21.1-q21.2	UniSTS
Cytogenetic Map	22	q12-q13	UniSTS
Cytogenetic Map	12	p11.21	UniSTS
Cytogenetic Map	5	p13.1	UniSTS
Cytogenetic Map	11	q21	UniSTS
Cytogenetic Map	17	q24.3	UniSTS
Cytogenetic Map	6	q25	UniSTS
Cytogenetic Map	9	p24.3	UniSTS
Cytogenetic Map	16	p12.2	UniSTS
Cytogenetic Map	3	q29	UniSTS
Cytogenetic Map	10	q26.1	UniSTS
Cytogenetic Map	4	q28.1	UniSTS
Cytogenetic Map	15	q15.1	UniSTS
Cytogenetic Map	15	q15.3	UniSTS
Cytogenetic Map	5	q32	UniSTS
Cytogenetic Map	3	q21.1	UniSTS
Cytogenetic Map	2	q37.1	UniSTS
Cytogenetic Map	2	q11.1	UniSTS
Cytogenetic Map	19	q13.12	UniSTS
Cytogenetic Map	14	q24.3	UniSTS
Cytogenetic Map	19	q13.33	UniSTS
Cytogenetic Map	19	p13.2	UniSTS
Cytogenetic Map	16	q24.1	UniSTS
Cytogenetic Map	19	p13.3	UniSTS
Cytogenetic Map	3	p21.3	UniSTS
Cytogenetic Map	17	p13.3	UniSTS
Cytogenetic Map	11	q13.2	UniSTS
Cytogenetic Map	9	q34.3	UniSTS
Cytogenetic Map	7	q	UniSTS
Cytogenetic Map	3	p26	UniSTS
Cytogenetic Map	22	q13.31	UniSTS
Cytogenetic Map	15	q11.2-q21.3	UniSTS
Cytogenetic Map	6	q16.2	UniSTS

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

adipose tissue	alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	entire extraembryonic component	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system
1196	2428	2672	2166	4837	1669	2298	4	576	1648	418	2191	6741	6061	52	3679	846	1729	1610	170


RefSeq Transcripts	NR_022014	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC025580	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC090527	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK096745	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY271964	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY271965	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY271966	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY271967	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC062412	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068263	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENST00000313559

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	15	45,511,151 - 45,556,102 (+)	Ensembl

Ensembl Acc Id:

ENST00000396644

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	15	45,511,151 - 45,556,102 (+)	Ensembl

Ensembl Acc Id:

ENST00000396645

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	15	45,511,151 - 45,556,102 (+)	Ensembl

Ensembl Acc Id:

ENST00000409454

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	15	45,511,136 - 45,556,730 (+)	Ensembl

Ensembl Acc Id:

ENST00000495658

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	15	45,511,153 - 45,519,664 (+)	Ensembl

Ensembl Acc Id:

ENST00000564594

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	15	45,529,734 - 45,555,900 (+)	Ensembl

Ensembl Acc Id:

ENST00000568669

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	15	45,521,836 - 45,586,290 (+)	Ensembl

Ensembl Acc Id:

ENST00000598619

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	15	45,555,482 - 45,555,971 (+)	Ensembl

RefSeq Acc Id:

NR_022014

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	15	45,511,136 - 45,556,730 (+)	NCBI
GRCh37	15	45,803,334 - 45,848,928 (+)	RGD
Celera	15	22,694,488 - 22,740,083 (+)	RGD
HuRef	15	22,626,368 - 22,671,536 (+)	ENTREZGENE
CHM1_1	15	45,921,545 - 45,967,131 (+)	NCBI
T2T-CHM13v2.0	15	43,319,297 - 43,364,888 (+)	NCBI

Sequence:

show sequence

ACCTAAGCGATGAAATCCAAAGGTGAATCTTTTGGTTGGTGATTTTGATGATAGCCACAAAGCAAGCAGGCTGTATGGTAGCCTTGAAAACCAACAGGCCACAATCACAGTGAAAACCTCAGGTTGGC
AGCCACTGGAGGATACAAAATGAGTTTGGATCTCCTTCAATGCCCCATTCCCAGAGAACTGTCATTATTTGACCTGCTGGTAGTTCCCTAAAGGACGTGCAAGGATGTTTTTATTTGACTGGACACTT
GAAGCTTGCCCTGTATGAACAGCCCCCATCTTCCCATGCTTGTCAAAAATCAGAGGCAACTAACACTGCGGCTTCCTGAGAGTCTCACTCTGTCACCCAGGCTGGAGAGCAATTGCACAAACACTTGG
CTCACTGCAGCCTCAACTTCTTGTCCTCAAGTGATCCTCCCACCTTAGCCTCCTAAGTAGCTGGGACCACAGGGAACTCCGGATGTGACTCCTGTTACATGAAAATGGAAGAGGTCAGAGTTGTCCAA
GAGGGAGGCCAGCCACATCCAGGCAGGGCCCCCATGGTCAGAACCCTGCTAGAGCCATCAAGGTCCCAGAGCTCCCAAGATGGTGGCAAGCCTTTTGTTCTCTGACCAGAGGTTCCTGGCCTCACGGA
TTCCAAGGAATGGAACCTTGGGCCATGCGTGCACTTGATTTTGCAGATGAGTCTGGAAGTGTTAGTTGCAAAGATATGCATTTACTTCTCTGGCTACAAAAAAGAATAGAAATGCACAAAGCAGAGCA
GTGTGAAGAAGAAGAGGCGATGACCCCTAGACCGACCAAAGCCCGTGCTCCACTGCCCAGTGCCTATGTCCCACCACTGTCGCTGCCACCCTGCCCGAGAGAAAGGCTGAAGGGGATGCTAAAGGAGA
TAAAACCAAGGTTAAGTAGGAACTGCAGAGAAGATCCACAAGGTTGTCTGCTAAACCTGCTCCTCCAAAGCCACAGCCGAAGCCCAGAAAGGCCTCTGCAAAGAAGAGAGAGAAGGTACCTACAGAGA
AGAAGGGAAAAGCTGATGCTGGCAAGGAGGGGAATAACCCTGCAGAAAATGGAGATGCCAAAACAGACTAGGCACAGAAAGCTAAAGGTGCTGGAGATGCCAAGTGAAGTGTGTGCATTTTTGATAAC
TGTGTACTTCTGGTGACTGTACAGTTTGAAATACTATTTTTTAATCAAGTTTTATAAAAATGCAGATTTTGTTTAGCTTTTTTTTTTTTTTTTAAGCTATGTTAGTACACAGAATACTTCATTGTTGT
TTTGGGGAGAAGGGCCATATGTCACTAATAGAAAGCCCCTGAAGCTGGACTGATGTGGGGAAAACACCTTTTCCTTCTGGTTTTGAGAGACTTCCTCTTGGGTCCCAGGAAGAGGGATTCCCTGACTT
TGATACACATGGCCACCTTGGTATAAAAGCCTTGTGGTATGGAAAAACAAATTCGTTTTTTATGTCCTCTTCTCTGTTTCTACCTTTCAGAATGGACTTAAATCCCTTAAACCCAGACATCTTCTGGG
ACCTGACCCCCAATAATTGGTTACCAGTGTGTCAGGCAATCTGGACTTTGCCCTCAAAAGAGCAGTGGTTCCTGTTTCTAGGTTGTGGATCTTCAGATAAATTCTGTCATTTTCCTTTCACTTCCTGA
AAGCCAGGGTCGGTTCATGAAAAGCTATGAAACAGCATGCTAAATGTGAAATGTCAACCCTCACTAAACTTTGCCGGTTCAGAGCATCAGATGAAGACTTCATTGGGTTTTACAGTGGCTTTCTGATT
TTTGGTAGTCCATTGAAGAAGGGAGTTTGAAAGTTGTTGTATACTGTTAACGATTGTCTGCCCATGTCCTGCCCAAAATACCATGATTCTTTATGGAAATTATCTTTAATAAAGCTGGATACAGTTTG
GCTTGGG

hide sequence


GenBank Protein	AAP12643	(Get FASTA)	NCBI Sequence Viewer
	AAP12644	(Get FASTA)	NCBI Sequence Viewer
	AAP12645	(Get FASTA)	NCBI Sequence Viewer
	AAP12646	(Get FASTA)	NCBI Sequence Viewer
	BAC04856	(Get FASTA)	NCBI Sequence Viewer

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q86SG4-F1-model_v2	AlphaFold	Q86SG4	1-172	view protein structure

Database	Acc Id	Source(s)
COSMIC	HMGN2P46	COSMIC
Ensembl Genes	ENSG00000179362	Ensembl
GTEx	ENSG00000179362	GTEx
HGNC ID	HGNC:26817	ENTREZGENE
Human Proteome Map	HMGN2P46	Human Proteome Map
NCBI Gene	283651	ENTREZGENE
OMIM	611314	OMIM
PharmGKB	PA134909825	PharmGKB
UniProt	DPCA2_HUMAN	UniProtKB/Swiss-Prot
UniProt Secondary	Q495B5	UniProtKB/Swiss-Prot
	Q86SH8	UniProtKB/Swiss-Prot
	Q8N8I5	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2011-07-27	HMGN2P46	high mobility group nucleosomal binding domain 2 pseudogene 46	C15orf21	chromosome 15 open reading frame 21	Symbol and/or name change	5135510	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailable


InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailable


Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
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