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PRDM12 Gene

protein-coding GIFtS: 37

GC09P103027

PR domain containing 12
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database

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(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
About This Section

Aliases & Descriptions
PR domain containing 12¹ ²
PFM9² ³
PR domain-containing protein 12² ³
PR-domain containing protein 12²
PR domain zinc finger protein 12²
PR-domain zinc finger protein 12²

External Ids:	HGNC: 13997¹	Entrez Gene: 59335²	Ensembl: ENSG00000130711⁷	UniProtKB: Q9H4Q4³

Export aliases for PRDM12 gene to outside databases

Previous GC identifers: GC09P124554 GC09P125086 GC09P126893 GC09P128816 GC09P130569 GC09P132529 GC09P133539

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: PRD12_HUMAN, Q9H4Q4

Function: May be involved in transcriptional regulation

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 60), Regulatory elements and Epigenetics data according to Qiagen and/or SABiosciences)
About This Section

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the PRDM12 gene promoter:
         HNF-1A   CUTL1   NRSF form 2   NRSF form 1   RORalpha2   CREB   deltaCREB   Nkx6-1   TBP   c-Rel
         Other transcription factors

Search SABiosciences Chromatin IP Primers for PRDM12

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for PRDM12

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 9q33-q34 Ensembl cytogenetic band: 9q34.12 HGNC cytogenetic band: 9q33-q34

PRDM12 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PRDM12 gene location

GeneLoc gene densities for chromosome 9 GeneLoc Exon Structure

GeneLoc location for GC09P103027: view genomic region (about GC identifiers)

Start:	103,027,137 bp from pter
End:	103,045,252 bp from pter
Size:	18,116 bases
Orientation:	plus strand

1 alternative location:

Chr9+ 133,539,981-133,558,368

RefSeq DNA sequence:

NC_000009.11 NT_035014.4

(According to ¹UniProtKB, neXtProt, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Millipore, Sigma-Aldrich, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, and/or ProSpec,
Biochemical Assays by Millipore, Sigma-Aldrich, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Dec 2010 and Entrez Gene, Antibodies by Millipore, Sigma-Aldrich, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, and/or Epitomics)
About This Section

UniProtKB/Swiss-Prot: PRD12_HUMAN, Q9H4Q4 (See protein sequence)

Recommended Name: PR domain zinc finger protein 12

Size: 367 amino acids; 40403 Da

Subcellular location: Nucleus (Potential)

PDB structures from and Proteopedia :

3EP0 (3D)

Secondary accessions: A3KFK9

Explore the universe of human proteins at neXtProt for PRDM12: NX_Q9H4Q4

REFSEQ proteins: NP_067632.2

ENSEMBL proteins:

ENSP00000253008

Human Recombinant Proteins

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2 Gene Ontology (GO) cellular component terms (GO ID links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005622	intracellular	IEA	--
GO:0005634	nucleus	IEA	--

About this table

PRDM12 for ontologies About GeneDecksing

Antibodies for PRDM12:

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Assays for PRDM12:

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	Browse ELISAs and CLIAs at Uscn

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

PRDM12 for domains About GeneDecksing

5 InterPro domains/families:

IPR001214 SET_dom

IPR017126 Znf_PRDM12

IPR015880 Znf_C2H2-like

IPR013087 Znf_C2H2/integrase_DNA-bd

IPR007087 Znf_C2H2

Graphical View of Domain Structure for InterPro Entry Q9H4Q4

ProtoNet protein and cluster: Q9H4Q4

UniProtKB/Swiss-Prot: PRD12_HUMAN, Q9H4Q4

Similarity: Contains 3 C2H2-type zinc fingers

Similarity: Contains 1 SET domain

(According to UniProtKB, IUBMB,and/or Genatlas, Animal models from MGI Dec 24 2010,
shRNA from OriGene, Sigma-Aldrich, RNAi from Millipore, siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich, microRNA from Sigma-Aldrich, Qiagen, SABiosciences, Clones from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, Cell Lines from GenScript, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene.)
About This Section

UniProtKB/Swiss-Prot: PRD12_HUMAN, Q9H4Q4

Function: May be involved in transcriptional regulation

Inhib. RNA:		Browse for Gene Knock-down Tools from Millipore
		Browse Nano Scale siRNA at Sigma-Aldrich Sigma-Aldrich siRNA for PRDM12 Sigma-Aldrich shRNA for PRDM12
		OriGene 29mer shRNA kits in GFP-retroviral vector: PRDM12 OriGene shRNA RFP: PRDM12 OriGene basic RS shRNA: PRDM12 OriGene siRNA: PRDM12
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miRNA:		Sigma-Aldrich microRNA Mimics for PRDM12 Browse microRNA target validation systems at Sigma-Aldrich
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of PRDM12
		8 SABiosciences Assays for microRNAs that regulate PRDM12:
		hsa-miR-577 hsa-miR-582-5p hsa-miR-656 hsa-miR-300 hsa-miR-381 hsa-miR-618 hsa-miR-1299 hsa-miR-1284

Gene
Editing:

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Cell
Lines:

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4 Gene Ontology (GO) molecular function terms (GO ID links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003677	DNA binding	IEA	--
GO:0005515	protein binding	IEA	--
GO:0008270	zinc ion binding	IEA	--
GO:0046872	metal ion binding	IEA	--

About this table

PRDM12 for ontologies About GeneDecksing

(Pathways according to Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB, Sets of similar genes according to GeneDecks, PCR Arrays from SABiosciences, Proteins Network according to SABiosciences, Sigma-Aldrich, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene).
About This Section

SABiosciences Custom Pathway-Focused PCR Arrays for PRDM12

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for PRDM12

2 Gene Ontology (GO) biological process terms (GO ID links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0022008	neurogenesis	IEA	--
GO:0045449	regulation of transcription	IEA	--

About this table

PRDM12 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse Small Molecules at Sigma-Aldrich

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for PRDM12

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Millipore,
siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene, microRNA from Sigma-Aldrich, Qiagen, SABiosciences,
Tagged/untagged cDNA clones from OriGene, Sigma-Aldrich, GenScript, Primers from OriGene and/or SABiosciences)
About This Section

Inhib. RNA:		Browse for Gene Knock-down Tools from Millipore
		Browse Nano Scale siRNA at Sigma-Aldrich Sigma-Aldrich siRNA for PRDM12 Sigma-Aldrich shRNA for PRDM12
		OriGene 29mer shRNA kits in GFP-retroviral vector: PRDM12 OriGene shRNA RFP: PRDM12 OriGene basic RS shRNA: PRDM12 OriGene siRNA: PRDM12
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of PRDM12

miRNA:		Sigma-Aldrich microRNA Mimics for PRDM12 Browse microRNA target validation systems at Sigma-Aldrich
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of PRDM12
		8 SABiosciences Assays for microRNAs that regulate PRDM12:
		hsa-miR-577 hsa-miR-582-5p hsa-miR-656 hsa-miR-300 hsa-miR-381 hsa-miR-618 hsa-miR-1299 hsa-miR-1284

Clones:		Browse FLAG tag genes at Sigma-Aldrich
		OriGene GFP tagged cDNA clones in CMV expression vector: PRDM12 OriGene Myc/DDK tagged cDNA clones in CMV expression vector: PRDM12 OriGene untagged cDNA clones in CMV expression vector: PRDM12 Browse 3'-UTR reporter clones for miRNA target validation Browse OriGene MicroRNA Expression Plasmids
		GenScript cDNA clone with any tag delivered in your preferred vector: PRDM12

Primers:		OriGene genome-wide validated SYBR primer pairs: PRDM12 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay for PRDM12: PPH16051A

REFSEQ mRNAs for PRDM12 gene:

NM_021619.2

Additional cDNA sequence: AY004252.2

1 DOTS entry:

DT.86835748

7 AceView cDNA sequences:

BE294489 NM_021619 AY004252 AW409624 BX114816 AW409886 AA974575

highest scoring ESTs for PRDM12:

AA974575 AW409624 AW409886 AY004252 BE294489 BX114816 NM_021619 AA199691 AA199799 AW409622

Unigene Cluster for PRDM12:

PR domain containing 12

Hs.495311 [show with all ESTs]

Unigene Representative Sequence: AY004252

GeneLoc Exon Structure

1 Ensembl transcript including schematic representation, and UCSC links where relevant:

ENST00000253008(uc004bzt.1)

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 228 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Primers from OriGene and/or SABiosciences )
About This Section

PRDM12 expression in normal and diseased human tissues

¹ / ² / ³

2 probe-sets matching PRDM12 gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
220894_x_at²^{, 3}	U133-A	1	0.46	1.00	--	--	NM_021619	0.60	1.00	0.82	1
220894_x_at²	U133Plus2	1	0.46	1.00	--	--	--	--	--	--	--

About this table
Data from Genenote (Publications) and GNF BioGPS
About these images

PRDM12 gene electronic northern expression

About these images

CGAP SAGE TAG: GTGCTGTGAG

SOURCE GeneReport for Unigene cluster: Hs.495311

Primers:		OriGene genome-wide validated SYBR primer pairs: PRDM12 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay for PRDM12: PPH16051A

SABiosciences Custom PCR Arrays for PRDM12

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Dec 24 2010, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section

Orthologs for PRDM12 gene from 5/8 species (see all 8)

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	PRDM12¹	--	PR domain containing 12	94.98(n) 98.9(a)	608616 XM_845693.1 XP_850786.1
chimpanzee (Pan troglodytes)	PRDM12¹	--	PR domain containing 12	99.54(n) 100(a)	473075 XM_528445.2 XP_528445.2
cow (Bos taurus)	PRDM12¹	--	PR domain containing 12	94.09(n) 98.89(a)	618320 XM_870651.2 XP_875744.2
rat (Rattus norvegicus)	Prdm12¹	--	PR domain containing 12	90.5(n) 98.63(a)	688699 XM_001067974.1 XP_001067974.1
mouse (Mus musculus)	Prdm12^{1 , 5}	2 (21.85 cM)⁵	PR domain containing 12^{1, 5}	91.3(n)¹ 98.63(a)¹	381359¹ XM_355325.5¹ XP_355325.5¹

About this table Species with no ortholog for PRDM12

ENSEMBL Gene Tree for PRDM12 (if available)

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
About This Section

Paralogs for PRDM12 gene

PRDM6² PRDM14² PRDM4²

PRDM12 for paralogs About GeneDecksing

(SNPs according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section

SNP ID	Valid	Chr 9 pos	Sequence	Recs	AA Chg	Type	More	Recs	Pop	Total sample
Genomic Data				Transcription Related Data				Allele Frequencies
			--	--	--		--	--
rs894241^1,2	C,F,A,	133553462(-)	`TGTTCC/TGGAAA`	1	--	int¹		14	EA NA NS WA	942
rs894242^1,2	C,F,A,	133553287(-)	`GAGTCC/TAGTTC`	1	--	int¹		10	NS EA WA	890
rs894243^1,2	C,F,A,	133553187(-)	`AGGATG/ATTGGT`	1	--	int¹		11	NA EA NS WA	874
rs1545229^1,2	C,F,O,A,H,	133550133(-)	`ATTGTG/ATAAAC`	1	--	int¹		20	NS EA NA WA	1366
rs1866974^1,2	C,A,H,	133541156(-)	`AAAGGG/TGGGGG`	1	--	int¹ trp³		3	NA	76
rs2027386^1,2	C,H,	133558282(-)	`TATATC/TACAGT`	1	--	ut3¹		5	NA WA	16
rs2277185^1,2	C,F,	133543981(-)	`GGACCT/ACACTA`	1	--	int¹		6	NS EA NA	578
rs2277186^1,2	C,F,	133543980(-)	`GACCTC/AACTAT`	1	--	int¹		5	EA NS NA	458
rs2313583^1,2	C,A,	133539126(+)	`ACTGTG/AGCGGC`	1	--	ng5¹		5	NA WA	128
rs2313584^1,2	C,F,	133542920(+)	`CCAGCC/TCCCCC`	1	--	int¹		2	NA	4

About this table

HapMap Linkage Disequilibrium images for PRDM12 (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for PRDM12: --

QIAGEN SeqTarget long-range PCR primers for resequencing PRDM12

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, LSDB, HGMD, GAD, HuGE Navigator, and/or TGDB.)
About This Section

(Possibly Related Articles in Doctor's Guide)
About This Section

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶UniProtKB/TrEMBL, and/or ⁷Novoseek)
About This Section

6 PubMed articles for PRDM12 gene integrated from 7 sources:
(articles sorted by number of sources associating them with PRDM12)

A potential role for PRDM12 in the pathogenesis of chronic myeloid leukaemia with derivative chromosome 9 deletion. (PubMed id 14523459)^{1, 3} Reid A.G. and Nacheva E.P. (2004)
DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)² Humphray S.J.... Dunham I. (2004)
SET domains and histone methylation. (PubMed id 14675547)¹ Xiao B....Gamblin S.J. (2003)
The prototypical 4.1R-10-kDa domain and the 4.1g-10-kDa paralog mediate fodrin-actin complex formation. (PubMed id 11274145)¹ Kontrogianni-Konstantopoulos A....Huang S.C. (2001)
Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )² Aoki H.... Hino O. (2000)
The yin-yang of PR-domain family genes in tumorigenesis. (PubMed id 10668202)¹ Jiang G.L. and Huang S. (2000)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 59335	HGNC: 13997	AceView: PRDM12	Ensembl:ENSG00000130711	euGenes: HUgn59335
ECgene: PRDM12	H-InvDB: PRDM12

(According to HUGE)
About This Section

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Intellectual Property for PRDM12 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from XenneX, Inc.)

About This Section

Patent Information for PRDM12 gene:
Search GeneIP for patents involving PRDM12

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or Enzo Life Sciences)
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	miRNA Expression Plasmids

	QIAGEN Custom miScript Target Protector blocks miRNA-binding site of PRDM12
	SeqTarget long-range PCR primers for resequencing PRDM12
	QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for PRDM12
	QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of PRDM12

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PRDM12 Gene

protein-coding GIFtS: 37

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PRDM12 Gene

protein-coding GIFtS: 37

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Pathways & Interactions
for PRDM12 gene

Drugs & Compounds
for PRDM12 gene

Transcripts
for PRDM12 gene

Expression
for PRDM12 gene

Orthologs
for PRDM12 gene

Paralogs
for PRDM12 gene

Genomic Variants
for PRDM12 gene

Disorders & Mutations
for PRDM12 gene

Medical News
for PRDM12 gene

Publications
for PRDM12 gene

Intellectual Property
for PRDM12 gene

Products
for PRDM12 gene