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TPRXL Gene

pseudogene   GIFtS: 32
GCID: GC03P013978

Tetra-Peptide Repeat Homeobox-Like

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Tetra-Peptide Repeat Homeobox-Like1 2

External Ids:    HGNC: 321781   Entrez Gene: 3488252   Ensembl: ENSG000001804387   OMIM: 6111675   UniProtKB: Q17RH73   
ORGUL members:         

Export aliases for TPRXL gene to outside databases

Previous GC identifers: GC03P013954 GC03P013912


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for TPRXL Gene:
Homeobox genes encode DNA-binding proteins, many of which are thought to be involved in early embryonic
development. Homeobox genes encode a DNA-binding domain of 60 to 63 amino acids referred to as the homeodomain.
This pseudogene is a member of the TPRX homeobox gene family. (provided by RefSeq, Jul 2008)

GeneCards Summary for TPRXL Gene:
TPRXL (tetra-peptide repeat homeobox-like) is a pseudogene, and is affiliated with the lncRNA class.




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000003.11  NC_018914.2  NT_022517.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the TPRXL gene promoter:
         MZF-1   p53   AML1a   GR-beta   Cart-1   CUTL1   Cdc5   c-Ets-1   YY1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TPRXL


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

Entrez Gene cytogenetic band: 3p25.1   Ensembl cytogenetic band:  3p25.1   HGNC cytogenetic band: 3p25.1

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

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P013978:  view genomic region     (about GC identifiers)

Start:
13,978,756 bp from pter      End:
14,124,311 bp from pter
Size:
145,556 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: TPRXL_HUMAN, Q17RH7 (See protein sequence)
Recommended Name: Putative protein TPRXL  
Size: 258 amino acids; 24139 Da
Caution: Could be the product of a pseudogene
Secondary accessions: Q8NAM5

Explore the universe of human proteins at neXtProt for TPRXL: NX_Q17RH7

Explore proteomics data for TPRXL at MOPED


See TPRXL Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


ENSEMBL proteins: 
 ENSP00000437227   ENSP00000435853   ENSP00000435219   ENSP00000322097   ENSP00000436919  
 ENSP00000435227   ENSP00000400448   ENSP00000435438   ENSP00000400824   ENSP00000432662  
 ENSP00000435511  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
PRD: Homeoboxes / PRD class

ProtoNet protein and cluster: Q17RH7


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus2
cytosol1
extracellular1
mitochondrion1

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TPRXL
Interactions:

    Search GeneGlobe Interaction Network for TPRXL

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
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Browse Tocris compounds for TPRXL



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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Unigene Clusters for TPRXL:

Tetra-peptide repeat homeobox-like
Hs.529180  [show with all ESTs], Hs.638296
Unigene Representative Sequences: NR_002223, BC027729
12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000532880 ENST00000530586 ENST00000532753 ENST00000524375 ENST00000326972(uc011avd.2)
ENST00000529129 ENST00000528312 ENST00000424053(uc021wtk.1 uc003byg.3)
ENST00000528067 ENST00000429201 ENST00000532924 ENST00000528040
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Additional mRNA sequence: BC027729.2 

6 DOTS entries:

DT.101978527  DT.40232462  DT.100718525  DT.99935760  DT.120844139  DT.120844141 

Selected AceView cDNA sequences (see all 29):

BM764893 CR613670 AI453103 BX111860 BU754588 AW303358 BM764898 AX747539 
BG481805 BX371689 BC027729 CD109930 AK092426 BM764892 BX379920 CF994921 
BX379919 BC016304 CB959908 BG001685 BM811485 AW138905 R82191 CB993262 

GeneLoc Exon Structure


(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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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TPRXL expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TTAATTGAAC
TPRXL Expression
About this image


TPRXL expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 3) fully expand
 
 Ovary (Reproductive System)
         Secondary Oocyte Antral Follicle
 
 Gonad
         Secondary Oocyte Antral Follicle
 
 Placenta (Extraembryonic Tissues)
TPRXL Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TPRXL Protein Expression

SOURCE GeneReport for Unigene clusters: Hs.529180 Hs.638296
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TPRXL

(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)
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This gene was present in the common ancestor of eukaryotes.

Orthologs for TPRXL gene from 2 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Obox35 oocyte specific homeobox 3   --   7 (8.53 cM) 15625302 
wheat
(Triticum aestivum)
Liliopsida Ta.228192 Triticum aestivum transcribed sequence with weak similarity more 71.43(n)    CD874909.1 


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

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

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for TPRXL (see all 2471)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 3 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1159472471,2
C,F--13978968(+) GACCAG/AGACGC 1 -- nc-transcript-variant1Minor allele frequency- A:0.03WA 118
rs1877127671,2
--13979106(+) GACTTG/TGGGTG 1 -- int10--------
rs1456011871,2
--13979136(+) GCCCTA/GGTTAC 1 -- int10--------
rs1932195331,2
C--13979176(+) TCACAA/GCAGAT 1 -- int10--------
rs1856292481,2
--13979265(+) TTTTTC/TTTTGA 1 -- int10--------
rs1381220871,2
--13979309(+) GCAGCA/GGCACC 1 -- int10--------
rs1884653791,2
--13979371(+) TCAGCC/TTCCCG 1 -- int10--------
rs1494701741,2
--13979493(+) TGATCC/TGCCCA 1 -- int10--------
rs1153776421,2
C,F--13979557(+) ATCTCC/TTAGGT 1 -- int11Minor allele frequency- T:0.02WA 118
rs1438473271,2
--13979742(+) TTCAAA/GTGATT 1 -- int10--------

HapMap Linkage Disequilibrium report for TPRXL (13978756 - 14124311 bp)

Structural Variations
     Database of Genomic Variants (DGV) 10 variations for TPRXL:    About this table    
Variant IDTypeSubtypePubMed ID
esv2629351CNV Deletion19546169
esv2724945CNV Deletion23290073
esv2584514CNV Insertion19546169
esv273722CNV Insertion20981092
nsv512797CNV Insertion21212237
nsv3711CNV Insertion18451855
esv269558CNV Insertion20981092
nsv526467CNV Loss19592680
nsv876550CNV Loss21882294
esv34163CNV Loss18971310

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DNA2.0 Custom Variant and Variant Library Synthesis for TPRXL

(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.)
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OMIM gene information: 611167    OMIM disorders: --


Find genes that share disorders with TPRXL           About GenesLikeMe


Export disorders for TPRXL gene to outside databases

(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)
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PubMed articles for TPRXL gene integrated from 10 sources:
(articles sorted by number of sources associating them with TPRXL)
    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. (Nat. Genet. 2004)
  2. Genetic variants and environmental factors associated with hormonal markers of ovarian reserve in Caucasian and African American women. (PubMed id 22116950)1 Schuh-Huerta S.M....Reijo Pera R.A. (Hum. Reprod. 2012)
  3. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
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)
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Entrez Gene: 348825 HGNC: 32178 AceView: FLJ35107 Ensembl:ENSG00000180438 euGenes: HUgn348825
ECgene: TPRXL H-InvDB: TPRXL

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for TPRXL Pharmacogenomics, SNPs, Pathways

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

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



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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