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TRNP1 Gene

protein-coding   GIFtS: 35
GCID: GC01P027320

TMF1-Regulated Nuclear Protein 1

(Previous name: chromosome 1 open reading frame 225)
(Previous symbol: C1orf225)
  See related diseases
at  

(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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Aliases
TMF1-Regulated Nuclear Protein 11 2
C1orf2251 2 3
Chromosome 1 Open Reading Frame 2251
TNRP2
TMF-Regulated Nuclear Protein 12
TRNP3

External Ids:    HGNC: 343481   Entrez Gene: 3886102   Ensembl: ENSG000002533687   UniProtKB: Q6NT893   

Export aliases for TRNP1 gene to outside databases

Previous GC identifers: GC01P027195 GC01P025575


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TRNP1 Gene:
TRNP1 (TMF1-regulated nuclear protein 1) is a protein-coding gene. Diseases associated with TRNP1 include cerebritis, and neuronitis.

UniProtKB/Swiss-Prot: TRNP1_HUMAN, Q6NT89
Function: DNA-binding factor that regulates the expression of a subset of genes and plays a key role in
tangential, radial, and lateral expansion of the brain neocortex. Regulates neural stem cells proliferation and
the production of intermediate neural progenitors and basal radial glial cells affecting the process of cerebral
cortex gyrification. May control the proliferation rate of cells by regulating their progression through key
cell-cycle transition points (By similarity)




(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:
NC_000001.11  NT_032977.10  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TRNP1 gene promoter:
         RP58   HOXA3   Bach2   Olf-1   Lmo2   HNF-4alpha1   GATA-1   CREB   HEN1   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTRNP1 promoter sequence
   Search Chromatin IP Primers for TRNP1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TRNP1


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

Entrez Gene cytogenetic band: 1p36.11   Ensembl cytogenetic band:  1p36.11   HGNC cytogenetic band: 1p36.11

TRNP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRNP1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P027320:  view genomic region     (about GC identifiers)

Start:
27,320,195 bp from pter      End:
27,327,389 bp from pter
Size:
7,195 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, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: TRNP1_HUMAN, Q6NT89 (See protein sequence)
Recommended Name: TMF-regulated nuclear protein 1  
Size: 227 amino acids; 23482 Da
Subunit: Interacts with TMF1; may regulate TRNP1 proteasomal degradation (By similarity)
Developmental stage: Expression is detected in the ventricular zone and neuronal layers of the developing cerebral
cortex at 12, 18 and 21 gestation weeks. Differences in regional expression seem to correlate with the process of
gyrification of the cortex. Highly expressed in germinal layers of the precentral and parahippocampal gyri, that
exhibit little radial expansion and folding, and weakly expressed in germinal layers of the occipital and
temporal lobes, that undergo greater expansion and folding

Explore the universe of human proteins at neXtProt for TRNP1: NX_Q6NT89

Explore proteomics data for TRNP1 at MOPED

Post-translational modifications: 

  • Ubiquitinated, leading to its degradation by the proteasome (By similarity)1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See TRNP1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001013664.1  
    ENSEMBL proteins: 
     ENSP00000429216   ENSP00000436467  

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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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    ProtoNet protein and cluster: Q6NT89


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TRNP1_HUMAN, Q6NT89
    Function: DNA-binding factor that regulates the expression of a subset of genes and plays a key role in
    tangential, radial, and lateral expansion of the brain neocortex. Regulates neural stem cells proliferation and
    the production of intermediate neural progenitors and basal radial glial cells affecting the process of cerebral
    cortex gyrification. May control the proliferation rate of cells by regulating their progression through key
    cell-cycle transition points (By similarity)

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ISS--
    GO:0005515protein binding ----
         
    TRNP1 for ontologies           About GeneDecksing


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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 UniProtKB/Swiss-Prot
    TRNP1_HUMAN, Q6NT89: Nucleus (By similarity)

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ISS--
    GO:0005719colocalizes with nuclear euchromatin ISS--

    TRNP1 for ontologies           About GeneDecksing


    (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 TRNP1
    Interactions:

        Search GeneGlobe Interaction Network for TRNP1

    Gene Ontology (GO): Selected biological process terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated IEA--
    GO:0007049cell cycle IEA--
    GO:0021696cerebellar cortex morphogenesis ISS--
    GO:0042127regulation of cell proliferation ISS--

    TRNP1 for ontologies           About GeneDecksing



    (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
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      Browse compounds at ApexBio 

    Browse Tocris compounds for TRNP1



    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for TRNP1 gene: 
    NM_001013642.2  

    Unigene Cluster for TRNP1:

    TMF1-regulated nuclear protein 1
    Hs.355747  [show with all ESTs]
    Unigene Representative Sequence: NM_001013642
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000522111(uc001bnj.4) ENST00000531285
    miRNA
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    hsa-miR-181c hsa-miR-4251 hsa-miR-877* hsa-miR-4314 hsa-miR-1276 hsa-miR-3658 hsa-miR-296-5p hsa-miR-28-5p
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    Additional mRNA sequence: BC069216.1 

    3 DOTS entries:

    DT.92420466  DT.95363667  DT.92420465 

    Selected AceView cDNA sequences (see all 72):

    AW151636 AW051390 BM310453 AI066629 BQ189050 BE219163 AI377954 BE671797 
    BM718216 BM310758 BG036482 AI366714 AW663347 AA532548 AA379296 AI093549 
    BM820130 CK904126 AI942335 AI817060 AI435085 AI970519 AA037766 BM021923 

    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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    TRNP1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGGTTCTGAG
    TRNP1 Expression
    About this image


    TRNP1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Neurons
             Mature Rod Bipolar Cells Inner Nuclear Layer
     
     Eye (Sensory Organs)
             Mature Rod Bipolar Cells Inner Nuclear Layer
    TRNP1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TRNP1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.355747
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    In Situ
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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)
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    This gene was present in the common ancestor of human and mouse.

    Orthologs for TRNP1 gene from Selected species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Trnp11 , 5 TMF1-regulated nuclear protein 11, 5 81.61(n)1
    83.41(a)1
      4 (66.25 cM)5
    695391  NM_001081156.21  NP_001074625.11 
     1334911005 


    ENSEMBL Gene Tree for TRNP1 (if available)
    TreeFam Gene Tree for TRNP1 (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 TRNP1 (see all 146)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1820064571,2
    --27318251(+) ATGGGA/GGGAGG 1 -- us2k10--------
    rs1131884791,2
    C,F--27318512(+) AGTGTT/GTGGTA 1 -- us2k12Minor allele frequency- G:0.03CSA WA 119
    rs1482977281,2
    --27318609(+) TCCCAC/GATAAA 1 -- us2k10--------
    rs1862195961,2
    --27318621(+) AACGTA/CCCTCC 1 -- us2k10--------
    rs1137563061,2
    C,F--27318929(+) GCTGGA/GACTAC 1 -- us2k12Minor allele frequency- G:0.16CSA WA 119
    rs1414891871,2
    --27319430(+) GCCACC/TGCGCC 1 -- us2k10--------
    rs783458981,2
    F--27319570(+) GGCTCA/GGCGGC 1 -- us2k11Minor allele frequency- G:0.01NA 120
    rs1898054901,2
    --27319695(+) CCCTAC/GTGAGG 1 -- us2k10--------
    rs1456688351,2
    --27319791(+) GAGCAC/TGGCAC 1 -- us2k10--------
    rs1814227231,2
    --27319822(+) TTCTAC/GCCCAG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for TRNP1 (27320195 - 27327389 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for TRNP1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv870497CNV Loss21882294
    nsv834524CNV Gain+Loss17160897

    Site Specific Mutation Identification with PCR Assays
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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.)
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    2 diseases for TRNP1:    
    About MalaCards
    cerebritis    neuronitis


    TRNP1 for disorders           About GeneDecksing


    Export disorders for TRNP1 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 TRNP1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with TRNP1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Trnp1 regulates expansion and folding of the mammalian cerebral cortex by control of radial glial fate. (PubMed id 23622239)1, 2 Stahl R....Goetz M. (Cell 2013)
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    3. trnp: A conserved mammalian gene encoding a nuclear protein that accelerates cell-cycle progression. (PubMed id 16792503)1 Volpe M....Nir U. (DNA Cell Biol. 2006)
    4. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)

    (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: 388610 HGNC: 34348 AceView: LOC388610 Ensembl:ENSG00000253368 euGenes: HUgn388610
    ECgene: TRNP1 H-InvDB: TRNP1

    (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 TRNP1 Pharmacogenomics, SNPs, Pathways
    Protein Spotlighthttp://web.expasy.org/spotlight/back_issues/152/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for TRNP1 gene:
    Search GeneIP for patents involving TRNP1

    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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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