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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SMEK3P Gene

pseudogene   GIFtS: 30
GCID: GC0XM027478

SMEK homolog 3, suppressor of mek1 (Dictyostelium) pseudogene
  Search for SMEK3P
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Biological research products
for SMEK3P    

Aliases
for SMEK3P gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
SMEK Homolog 3, Suppressor Of Mek1 (Dictyostelium) Pseudogene1 2
FLFL3P1 2
Smk11
FLJ328671

External Ids:    HGNC: 331461   Entrez Gene: 1394202   Ensembl: ENSG000002249607   UniProtKB: Q6ZMV53   
ORGUL members:         
NONCODE:n405621    

Export aliases for SMEK3P gene to outside databases

Previous GC identifers: GC0XM027389 GC0XM025217


Summaries
for SMEK3P gene

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

Genomic Views
for SMEK3P gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.1  NT_167197.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SMEK3P gene promoter:
         TBP   FOXD1   STAT5A   Cdc5   RORalpha1   MEF-2A   POU2F1   POU2F1a   Chx10   aMEF-2   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SMEK3P


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

Entrez Gene cytogenetic band: Xp21.3   Ensembl cytogenetic band:  Xp21.3   HGNC cytogenetic band: Xp21.3

SMEK3P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMEK3P gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM027478:  view genomic region     (about GC identifiers)

Start:
 27,478,328 bp from pter      End:
 27,481,458 bp from pter
Size:
 3,131 bases      Orientation:
 minus strand

Proteins
for SMEK3P gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: SMEK3_HUMAN, Q6ZMV5 (See protein sequence)
Recommended Name: Putative SMEK homolog 3  
Size: 832 amino acids; 95776 Da
Caution: Could be the product of a pseudogene
Sequence caution: Sequence=BAB71482.1; Type=Erroneous initiation;
Secondary accessions: Q96M31
Alternative splicing: 2 isoforms:  Q6ZMV5-1   Q6ZMV5-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SMEK3P: NX_Q6ZMV5

SMEK3P Protein expression data from MOPED and PaxDb: --

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Protein Domains /
Families
for SMEK3P gene

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
SMEK3P for domains           About GeneDecksing

2 InterPro domains/families:
 IPR006887 DUF625
 IPR016024 ARM-type_fold

Graphical View of Domain Structure for InterPro Entry Q6ZMV5

ProtoNet protein and cluster: Q6ZMV5

UniProtKB/Swiss-Prot: SMEK3_HUMAN, Q6ZMV5
Similarity: Belongs to the SMEK family


Function
for SMEK3P gene

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section
miRNA
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Inhib. RNA
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In Situ Assay
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Pathways & Interactions
for SMEK3P gene

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SMEK3P

Drugs & Compounds
for SMEK3P gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for SMEK3P
Search CenterWatch for drugs/clinical trials and news about SMEK3P 

Transcripts
for SMEK3P gene

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

Unigene Cluster for SMEK3P:

SMEK homolog 3, suppressor of mek1 (Dictyostelium) pseudogene
Hs.350673  [show with all ESTs]
Unigene Representative Sequence: AK131475
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000412172(uc004dbu.1)

miRNA
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Inhib. RNA
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Primer
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Additional cDNA sequence: 

AK057429.1 AK131475.1 NR_002784.1 

2 DOTS entries:

DT.102820099  DT.91742320 

3 AceView cDNA sequences:

NM_207319 AK131475 AK057429 

GeneLoc Exon Structure


Expression
for SMEK3P gene

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

SMEK3P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: TGAACTTATA

Microarray
RNAseq (Illumina Body Map)
(100×FPKM)½
SAGE (Serial Analysis of Gene Expression)
About this image

SMEK3P expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
1 LifeMap In Vivo Development Anatomical Compartment/Cell 
Tissue Anatomical Compartment CellCategory (developmental path)
TestisSeminiferous TubulesSpermatidGerm Cells, Male Gametocytes
Expression: Positive    Negative     Selective marker
Experimental details: Curated     Microarrays     In-situ hybridization

Genevestigator expression for SMEK3P

SOURCE GeneReport for Unigene cluster: Hs.350673
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In Situ
Assay Products: 
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Orthologs
for SMEK3P gene

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section
This gene was present in the common ancestor of human and mouse.

Orthologs for SMEK3P gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification		 Gene Description Human
Similarity		 Orthology
Type		 Details
mouse
(Mus musculus)		 Mammalia Smek3-ps5 SMEK homolog 3, suppressor of mek1 (Dictyostelium), more   --   X (39.95 cM) 88729828 


ENSEMBL Gene Tree for SMEK3P (if available)
TreeFam Gene Tree for SMEK3P (if available) 

Paralogs
for SMEK3P gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

Genomic Variants
for SMEK3P gene

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/68 NCBI SNPs in SMEK3P are shown (see all 68)     About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance		Chr X posSequence#AA
Chg		TypeMore#Allele
freq		PopTotal
sample		More
----------
rs128357811,2
C,--27477835(+) ATCACA/TTGAGG 1 -- int11Minor allele frequency- T:0.00NA 2
rs1873221871,2
--27477947(+) TATGTG/TGGAGG 1 -- int10--------
rs1410384581,2
C--27478054(+) AAAAA-/AGTTAT 1 -- int10--------
rs120068871,2
C,F,H,--27478079(+) AacaaC/Tcacat 1 -- int110Minor allele frequency- T:0.07NS EA NA CSA 1085
rs610299901,2
C,--27478109(+) TGTGAT/CCACAC 1 -- int11Minor allele frequency- C:0.00WA 2
rs169878991,2
C,F,H,--27478358(+) TGAAAA/GTACAC 1 -- nc-transcript-variant14Minor allele frequency- G:0.86NA NS EA WA CSA 1343
rs557367361,2
C,--27478511(+) GGAAAT/GAATAC 1 -- nc-transcript-variant1Minor allele frequency- G:0.00WA 2
rs1834933311,2
--27478581(+) TAATAC/TATACC 1 -- nc-transcript-variant0--------
rs169879011,2
C,F,--27478651(+) TTTCCT/ATCCCA 1 -- nc-transcript-variant3Minor allele frequency- A:0.01NA 142
rs2002676711,2
--27478736(+) TACTG-/TTTTTT 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for SMEK3P (27478328 - 27481458 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for SMEK3P
     1 CNV: 73949

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Disorders / Diseases
for SMEK3P gene

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
   --

Publications
for SMEK3P gene

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed article for SMEK3P gene integrated from 9 sources:
(articles sorted by number of sources associating them with SMEK3P)		    Utopia: connect your pdf to the dynamic
world of online information

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)

External Searches for SMEK3P gene

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  
  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

Genome Databases showing SMEK3P gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 139420 HGNC: 33146 AceView: FLJ32867 Ensembl:ENSG00000224960 euGenes: HUgn139420
ECgene: SMEK3P H-InvDB: SMEK3P

Other Databases showing SMEK3P gene

(According to HUGE)
About This Section
   --

Specialized Databases showing SMEK3P gene

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

Intellectual Property
for SMEK3P gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for SMEK3P gene:
Search GeneIP for patents involving SMEK3P

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



Products
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About This Section

 
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