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TNP1 Gene

protein-coding   GIFtS: 58
GCID: GC02M217724

Transition Protein 1 (During Histone To Protamine Replacement)

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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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Aliases
Transition Protein 1 (During Histone To Protamine Replacement)1 2
STP-12 3
TP-12 3
TP12
Spermatid Nuclear Transition Protein 12

External Ids:    HGNC: 119511   Entrez Gene: 71412   Ensembl: ENSG000001182457   OMIM: 1902315   UniProtKB: P094303   

Export aliases for TNP1 gene to outside databases

Previous GC identifers: GC02M215821 GC02M216445 GC02M217688 GC02M217926 GC02M217549 GC02M217432 GC02M209578


(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 TNP1 Gene:
Transition protein-1 is a spermatid-specific product of the haploid genome which replaces histone and is itself
replaced in the mature sperm by the protamines (see PRM1, MIM 182880; PRM2, MIM 182890) (Luerssen et al., 1990
(PubMed 2249851)).(supplied by OMIM, Mar 2008)

GeneCards Summary for TNP1 Gene:
TNP1 (transition protein 1 (during histone to protamine replacement)) is a protein-coding gene.

UniProtKB/Swiss-Prot: STP1_HUMAN, P09430
Function: In the elongating spermatids of mammals, the conversion of nucleosomal chromatin to the compact,
non-nucleosomal form found in the sperm nucleus is associated with the appearance of a small set of basic
chromosomal transition proteins

Gene Wiki entry for TNP1 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NC_018913.2  NT_005403.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the TNP1 gene promoter:
         SRF   SRF (504 AA)   NF-E2 p45   LCR-F1   C/EBPalpha   YY1   Evi-1   AREB6   HSF2   NF-E2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTNP1 promoter sequence
   Search Chromatin IP Primers for TNP1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TNP1


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

Entrez Gene cytogenetic band: 2q35-q36   Ensembl cytogenetic band:  2q35   HGNC cytogenetic band: 2q35-q36

TNP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TNP1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M217724:  view genomic region     (about GC identifiers)

Start:
217,724,181 bp from pter      End:
217,724,787 bp from pter
Size:
607 bases      Orientation:
minus 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: STP1_HUMAN, P09430 (See protein sequence)
Recommended Name: Spermatid nuclear transition protein 1  
Size: 55 amino acids; 6424 Da

Explore the universe of human proteins at neXtProt for TNP1: NX_P09430

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • REFSEQ proteins: NP_003275.1  
    ENSEMBL proteins: 
     ENSP00000236979  

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    Search eBioscience for ELISAs for TNP1 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR001319 Nuclear_transition_prot1
     IPR020062 Nuclear_transition_prot1_CS

    Graphical View of Domain Structure for InterPro Entry P09430

    ProtoNet protein and cluster: P09430

    1 Blocks protein domain: IPB001319 Nuclear transition protein 1

    UniProtKB/Swiss-Prot: STP1_HUMAN, P09430
    Similarity: Belongs to the nuclear transition protein 1 family


    Find genes that share domains with TNP1           About GenesLikeMe


    (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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: STP1_HUMAN, P09430
    Function: In the elongating spermatids of mammals, the conversion of nucleosomal chromatin to the compact,
    non-nucleosomal form found in the sperm nucleus is associated with the appearance of a small set of basic
    chromosomal transition proteins

         Genatlas biochemistry entry for TNP1:
    transition protein 1 (in haploid spermatogenic cells during transition histone-protamine)

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IMP12743712
         
    Find genes that share ontologies with TNP1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for TNP1:
     Cell cycle / mitosis defect 

         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Tnp1):
     reproductive system 

    Find genes that share phenotypes with TNP1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Tnp1tm1Mlm for TNP1

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for TNP1
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for TNP1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for TNP1

    miRNA
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    miRTarBase miRNAs that target TNP1:
    hsa-mir-7-5p (MIRT025822)

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    Selected qRT-PCR Assays for microRNAs that regulate TNP1 (see all 10):
    hsa-miR-34c-5p hsa-miR-181c hsa-miR-449b hsa-miR-181a hsa-miR-181d hsa-miR-449a hsa-miR-34a hsa-miR-143
    SwitchGear 3'UTR luciferase reporter plasmidTNP1 3' UTR sequence
    Inhib. RNA
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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
    STP1_HUMAN, P09430: Nucleus. Chromosome
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000786nucleosome IDA12743712
    GO:0001673male germ cell nucleus IEA--
    GO:0005634nucleus ----

    Find genes that share ontologies with TNP1           About GenesLikeMe


    (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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    SuperPaths for TNP1 About    
    See pathways by source

    SuperPathContained pathways About
    1Transcription CREM signaling in testis
    Transcription CREM signaling in testis

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 GeneGo (Thomson Reuters) Pathway for TNP1
        Transcription CREM signaling in testis


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TNP1
    Interactions:

        Search GeneGlobe Interaction Network for TNP1

    STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

    5 Interacting proteins for TNP1 (P094303 ENSP000002369794) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PRKACAP176123, ENSP000003095914I2D: score=1 STRING: ENSP00000309591
    CSNK2A1P684003, ENSP000002172444I2D: score=1 STRING: ENSP00000217244
    PRKACBP226943, ENSP000003597194I2D: score=1 STRING: ENSP00000359719
    PRKACGP226123, ENSP000003664884I2D: score=1 STRING: ENSP00000366488
    PRKCAP172523, ENSP000002843844I2D: score=1 STRING: ENSP00000284384
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000012single strand break repair IDA12743712
    GO:0006337nucleosome disassembly IMP10781074
    GO:0006338chromatin remodeling IDA12743712
    GO:0006342chromatin silencing IEP11315969
    GO:0007275multicellular organismal development IEA--

    Find genes that share ontologies with TNP1           About GenesLikeMe



    (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
      Browse compounds at ApexBio 

    Browse Tocris compounds for TNP1 (STP1)

    4 Novoseek inferred chemical compound relationships for TNP1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    protamine 85.3 17 1395729 (1), 10194639 (1), 11315969 (1), 11732576 (1) (see all 10)
    paraffin 32.1 2 8605397 (1), 17683460 (1)
    gold 0 1 10194639 (1)
    serine 0 1 2040274 (1)



    Find genes that share compounds with TNP1           About GenesLikeMe



    (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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    REFSEQ mRNAs for TNP1 gene: 
    NM_003284.3  

    Unigene Cluster for TNP1:

    Transition protein 1 (during histone to protamine replacement)
    Hs.3017  [show with all ESTs]
    Unigene Representative Sequence: BM563653
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000236979(uc002vgk.3)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate TNP1 (see all 10):
    hsa-miR-34c-5p hsa-miR-181c hsa-miR-449b hsa-miR-181a hsa-miR-181d hsa-miR-449a hsa-miR-34a hsa-miR-143
    SwitchGear 3'UTR luciferase reporter plasmidTNP1 3' UTR sequence
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      QuantiFast Probe-based Assays in human, mouse, rat TNP1

    Additional mRNA sequence: BC029516.1 

    4 DOTS entries:

    DT.91690070  DT.120931743  DT.408516  DT.100776396 

    Selected AceView cDNA sequences (see all 70):

    AL037319 BE552039 CR601312 BF222983 BF062064 T29843 AL552806 AL037398 
    BF059332 AL038317 BE503890 AL037843 BX117749 NM_003284 AL552771 BX438872 
    BM552864 BC029516 AW197353 BE504726 AI652461 AI990830 AI018791 AI670962 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for TNP1    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b
    SP1:                              
    SP2:              -               


    ECgene alternative splicing isoforms for TNP1

    (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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    TNP1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGGAGGAGCA
    TNP1 Expression
    About this image


    TNP1 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
     
     Testis (Reproductive System)    fully expand to see all 7 entries
             XY Germ Cells Testis Cord
             Testis Interstitium
             testis ; cells in seminiferous ducts   
             sperm   
     
     Gonad
             XY Germ Cells Testis Cord
     
     Eye (Sensory Organs)
             Retina
    TNP1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

    SOURCE GeneReport for Unigene cluster: Hs.3017

    UniProtKB/Swiss-Prot: STP1_HUMAN, P09430
    Tissue specificity: Expressed by spermatids (at protein level)

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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 TNP1 gene from Selected species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tnp15 transition protein 1   --   1 (36.94 cM) 73015083 


    ENSEMBL Gene Tree for TNP1 (if available)
    TreeFam Gene Tree for TNP1 (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 TNP1 (see all 74)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1150472951,2
    F--217723683(+) TTTACA/CAAGAA 1 -- int11Minor allele frequency- C:0.01WA 118
    rs1471798611,2
    --217723693(+) ACATGC/TTGGTC 1 -- int10--------
    rs126943981,2
    C,F,A--217723737(+) CTAATC/ACTGCC 1 -- int112Minor allele frequency- A:0.46NA WA CSA EA 374
    rs1405541901,2
    C--217723928(+) TGAATA/GCATTT 1 -- int10--------
    rs1422165001,2
    --217723943(+) CTTTTA/TTATCT 1 -- int10--------
    rs1508077531,2
    --217724078(+) TTTGAC/TATTTT 1 -- int10--------
    rs1390152401,2
    --217724209(+) AGATGC/TTGGGG 1 -- ut310--------
    rs1894896421,2
    --217724212(+) TGTTGA/GGGAAA 1 -- ut310--------
    rs1477135721,2
    C,F--217724393(+) GCTCAC/TAAGTG 2 L syn11Minor allele frequency- T:0.00NA 4550
    rs2013946031,2
    --217724404(+) GGAGCA/GGTAAT 2 R C mis10--------

    HapMap Linkage Disequilibrium report for TNP1 (217724181 - 217724787 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for TNP1: --
    Human Gene Mutation Database (HGMD): TNP1
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing TNP1
    DNA2.0 Custom Variant and Variant Library Synthesis for TNP1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 190231    OMIM disorders: --

    2 diseases from the University of Copenhagen DISEASES database for TNP1:
    Male infertility     Infertility

    Find genes that share disorders with TNP1           About GenesLikeMe

    3 Novoseek inferred disease relationships for TNP1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    infertility male 61.7 1 16291974 (1)
    azoospermia 51.6 6 17683460 (4)
    infertility 34.5 2 16989827 (1)

    Genetic Association Database (GAD): TNP1
    Human Genome Epidemiology (HuGE) Navigator: TNP1 (4 documents)

    Export disorders for TNP1 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 TNP1 gene, integrated from 10 sources (see all 54):
    (articles sorted by number of sources associating them with TNP1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Nucleotide sequence of the gene for human transition protein 1 and its chromosomal localization on chromosome 2. (PubMed id 2249851)1, 2, 3, 9 Luerssen H....Engel W. (Genomics 1990)
    2. Single-nucleotide polymorphisms and mutation analyses of the TNP1 and TNP2 genes of fertile and infertile human male populations. (PubMed id 16291974)1, 4, 9 Miyagawa Y.... Tanaka H. (J. Androl. 2005)
    3. Identification of novel polymorphisms in the nuclear protein genes and their relationship with human sperm protamine deficiency and severe male infertility. (PubMed id 16989827)1, 4, 9 Aoki V.W....Carrell D.T. (Fertil. Steril. 2006)
    4. Expression of mRNA and protein of nucleoproteins during human spermiogenesis. (PubMed id 9809674)1, 2, 9 Steger K....Bergmann M. (Mol. Hum. Reprod. 1998)
    5. Genome-wide association study identifies four loci associated with eruption of permanent teeth. (PubMed id 21931568)1, 4 Geller F....Melbye M. (PLoS Genet. 2011)
    6. Evaluation of 172 candidate polymorphisms for association with oligozoospermia or azoospermia in a large cohort of men of European descent. (PubMed id 20378615)1, 4 Aston K.I....Carrell D.T. (Hum. Reprod. 2010)
    7. 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. (Genome Res. 2004)
    8. The nucleotide sequence of human transition protein 1 cDNA. (PubMed id 3412903)1, 2 Luerssen H.... Engel W. (Nucleic Acids Res. 1988)
    9. Quantitative assessment of transition proteins 1, 2 spermatid-specific linker histone H1-like protein transcripts in spermatozoa from normozoospermic and asthenozoospermic men. (PubMed id 17852044)1, 9 Jedrzejczak P....Jagodzinski P.P. (Arch. Androl. 2007)
    10. Nuclear transition protein 1 from ram elongating spermatids. Mass spectrometric characterization, primary structure and phosphorylation sites of two variants. (PubMed id 2040274)1, 9 Chirat F....SautiA"re P. (Eur. J. Biochem. 1991)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 7141 HGNC: 11951 AceView: TNP1 Ensembl:ENSG00000118245 euGenes: HUgn7141
    ECgene: TNP1 H-InvDB: TNP1

    (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 TNP1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for TNP1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for TNP1 gene:
    Search GeneIP for patents involving TNP1

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



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