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

TLX1NB Gene

protein-coding   GIFtS: 28
GCID: GC10M102840

TLX1 Neighbor

  Search for TLX1NB
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 4

Aliases
TLX1 Neighbor1 2     APT-B72
TDI2 3     Putative Protein TDI2
TLX1 Divergent Gene Protein2 3     Putative TLX1 Neighbor Protein2
TD12 5     

External Ids:    HGNC: 371831   Entrez Gene: 1000382462   Ensembl: ENSG000002363117   OMIM: 6127345   UniProtKB: P0CAT33   
ORGUL members:    fRNAdb10:FR195462 FR399740      
H-InvDB12:HIT000325667 HIT000325666    
NCBI13:Y11609 Y11608    
NONCODE14:n340125 n340126 n378189 n340124 n336275      
RNAdb15:HIV1640    

Export aliases for TLX1NB gene to outside databases

Previous GC identifer: GC10M096478


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

GeneCards Summary for TLX1NB Gene: 
TLX1NB (TLX1 neighbor) is a protein-coding gene, and is affiliated with the lncRNA class.

fRNAdb sequence ontology for TLX1NB:
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

View fRNAdb secondary structures for TLX1NB

(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000010.10  NC_018921.2  NT_030059.13  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for TLX1NB
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for TLX1NB

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TLX1NB


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

Entrez Gene cytogenetic band: 10q24   Ensembl cytogenetic band:  10q24.31   HGNC cytogenetic band: 10q24

TLX1NB Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TLX1NB gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M102840:  view genomic region     (about GC identifiers)

Start:
102,849,078 bp from pter      End:
102,890,903 bp from pter
Size:
41,826 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for TLX1NB

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: TLXNB_HUMAN, P0CAT3 (See protein sequence)
Recommended Name: Putative TLX1 neighbor protein  
Size: 122 amino acids; 13375 Da
Miscellaneous: Oriented in a head-to-head manner with TLX1/HOX11. Both genes share the same promoter with robust
bidirectional activity
Caution: Product of a dubious CDS prediction

Explore the universe of human proteins at neXtProt for TLX1NB: NX_P0CAT3

TLX1NB Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --

REFSEQ proteins: NP_001078867.1  
ENSEMBL proteins: 
 ENSP00000475001  

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

ProtoNet protein and cluster: P0CAT3


(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,
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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Animal Models:
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(Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TLX1NB

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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
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Browse Tocris compounds for TLX1NB (TLXNB)

Search CenterWatch for drugs/clinical trials and news about TLX1NB / TLXNB

(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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
2 fRNAdb Secondary structures:


REFSEQ mRNAs for TLX1NB gene: 
NM_001085398.1  

Unigene Cluster for TLX1NB:

TLX1 neighbor
Hs.662323  [show with all ESTs]
Unigene Representative Sequence: BC019674
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000445873(uc001ksv.3) ENST00000425505
miRNA
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Additional mRNA sequence: 

BC019674.1 Y11608.1 

2 DOTS entries:

DT.101975796  DT.40220038 

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™, 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

TLX1NB expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
TLX1NB Expression
About this image


SOURCE GeneReport for Unigene cluster: Hs.662323
    SABiosciences Custom PCR Arrays for TLX1NB
Primer
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In Situ
Assay Products:
 

 
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(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
  --

ENSEMBL Gene Tree for TLX1NB (if available)
TreeFam Gene Tree for TLX1NB (if available)

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

(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) 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

10/866 SNPs in TLX1NB are shown (see all 866)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 10 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1426286691,2
--102848723(+) TTTCCC/TTCCTT 1 -- ds50010--------
rs108835801,2
C,F,A,H--102848834(+) GCCTCG/ATCAGT 1 -- ds500121Minor allele frequency- A:0.36NS EA NA WA CSA 2345
rs1845752891,2
--102848856(+) GTTATA/GCCAGG 1 -- ds50010--------
rs618715311,2
C,F--102848905(+) GAACTG/CTGAGT 1 -- ds50016Minor allele frequency- C:0.26NA WA EA 364
rs1147188651,2
F--102848949(+) GGGTTC/TGTGGA 1 -- ds50011Minor allele frequency- T:0.03WA 118
rs797179081,2
--102848980(+) TGCCCA/TCAGTA 1 -- ds50011Minor allele frequency- T:0.00CSA 1
rs563136321,2
C--102848982(+) CCTCA-/CA/CG 
        
GTATT
1 -- ds50012NA CSA 4
rs1139347301,2
F--102849029(+) ACCCCG/ATCGCT 1 -- ds50012Minor allele frequency- A:0.03CSA WA 119
rs1879187871,2
--102849100(+) TTACTA/GCTTTA 1 -- ut310--------
rs1449721311,2
C--102849112(+) TGTTCG/TCAAAG 1 -- ut310--------

HapMap Linkage Disequilibrium report for TLX1NB (102849078 - 102890903 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for TLX1NB:    About this table     
Variant IDTypeSubtypePubMed ID
nsv895966CNV Loss21882294
nsv508603CNV Loss20534489
nsv831966CNV Gain17160897

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

TLX1NB for disorders           About MalaCards
OMIM gene information: 612734OMIM information: 603188 607499    

TLX1NB for disorders           About GeneDecksing


Export disorders for TLX1NB 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)
About This Section

PubMed articles for TLX1NB gene integrated from 9 sources:
(articles sorted by number of sources associating them with TLX1NB)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A promoter with bidirectional activity is located between TLX1/HOX11 and a divergently transcribed novel human gene. (PubMed id 17303350)1, 2, 3 Greene W.K....Bellgard M.I. (2007)
  2. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)1, 2 Deloukas P.... Rogers J. (2004)
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
  4. 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. (2002)
  5. (PubMed id 15103394)10 
  6. (PubMed id 18089548)10 
  7. (PubMed id 15608161)10 

(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)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 100038246 HGNC: 37183 Ensembl:ENSG00000236311 euGenes: HUgn100038246 ECgene: TLX1NB
H-InvDB: TLX1NB

(According to HUGE)
About This Section
  --

(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
NameDescription
PharmGKB entry for TLX1NB Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for TLX1NB gene:
Search GeneIP for patents involving TLX1NB

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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About This Section

 
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