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

PAMR1 Gene

protein-coding   GIFtS: 48
GCID: GC11M035453

peptidase domain containing associated with muscle regeneration...

 Explore 3 diseases affiliated with
PAMR1 via our new
 Human Malady Compendium 
Biological research products
for PAMR1
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Peptidase Domain Containing Associated With Muscle Regeneration 11 2     Regeneration-Associated Muscle Protease Homolog2 3
RAMP1 2 3     Inactive Serine Protease PAMR12
DKFZP586H21231 2     Regeneration Associated Muscle Protease2
Peptidase Domain-Containing Protein Associated With Muscle Regeneration 12 3     

External Ids:    HGNC: 245541   Entrez Gene: 258912   Ensembl: ENSG000001490907   UniProtKB: Q6UXH93   

Export aliases for PAMR1 gene to outside databases

Previous GC identifers: GC11M035410 GC11M035152


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

UniProtKB/Swiss-Prot: PAMR1_HUMAN, Q6UXH9
Function: May play a role in regeneration of skeletal muscle (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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000011.9  NC_018922.1  NT_009237.18  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PAMR1 gene promoter:
         AML1a   FOXF2   MIF-1   Nkx2-5   Nkx5-1   NF-AT   NF-AT2   FOXO4   NF-AT3   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPAMR1 promoter sequence
   Search SABiosciences Chromatin IP Primers for PAMR1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PAMR1


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

Entrez Gene cytogenetic band: 11p13   Ensembl cytogenetic band:  11p13   HGNC cytogenetic band: 11p13

PAMR1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PAMR1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M035453:  view genomic region     (about GC identifiers)

Start:
35,453,370 bp from pter      End:
35,551,848 bp from pter
Size:
98,479 bases      Orientation:
minus strand

(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: PAMR1_HUMAN, Q6UXH9 (See protein sequence)
Recommended Name: Inactive serine protease PAMR1 precursor  
Size: 720 amino acids; 80199 Da
Subcellular location: Secreted (Potential)
Caution: Although related to peptidase S1 family, lacks the conserved active Ser residue in position 665 which is
replaced by a Thr, suggesting that it has no protease activity
Sequence caution: Sequence=AAQ15224.1; Type=Frameshift; Positions=334;
Secondary accessions: Q5EBL7 Q5JPI4 Q6N062 Q71RE9 Q96JW2 Q9Y432
Alternative splicing: 2 isoforms:  Q6UXH9-1   Q6UXH9-2   

Explore the universe of human proteins at neXtProt for PAMR1: NX_Q6UXH9

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q6UXH9

  • PAMR1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001001991.1  NP_056245.2  

    ENSEMBL proteins: 
     ENSP00000278360   ENSP00000368158   ENSP00000433868   ENSP00000432591   ENSP00000433024  
     ENSP00000368156  

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    Uscn Proteins for PAMR1

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--


    PAMR1 for ontologies           About GeneDecksing



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

    PAMR1 for domains           About GeneDecksing

    5/7 InterPro domains/families (see all 7):
     IPR001314 Peptidase_S1A
     IPR000742 EG-like_dom
     IPR000436 Sushi_SCR_CCP
     IPR001254 Peptidase_S1
     IPR000859 CUB_dom

    Graphical View of Domain Structure for InterPro Entry Q6UXH9

    ProtoNet protein and cluster: Q6UXH9

    5 Blocks protein families:
    IPB000436 Sushi domain/SCR domain/CCP module
    IPB001254 Serine protease
    IPB001314 Chymotrypsin serine protease family (S1) signature
    IPB001881 EGF-like calcium-binding
    IPB006210 Type I EGF


    UniProtKB/Swiss-Prot: PAMR1_HUMAN, Q6UXH9
    Similarity: Belongs to the peptidase S1 family
    Similarity: Contains 1 CUB domain
    Similarity: Contains 1 EGF-like domain
    Similarity: Contains 1 peptidase S1 domain
    Similarity: Contains 2 Sushi (CCP/SCR) domains


    (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

    Function Summary:

         UniProtKB/Swiss-Prot: PAMR1_HUMAN, Q6UXH9
    Function: May play a role in regeneration of skeletal muscle (By similarity)
    Induction: Strongly down-regulated in muscle cell lines derived from biopsies of 5 Duchenne muscular dystrophy (DMD)
    patients compared to a normal muscle cell line

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate PAMR1:
    hsa-miR-4318
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    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PAMR1

    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity IEA--
    GO:0004252serine-type endopeptidase activity ----


    PAMR1 for ontologies           About GeneDecksing


    2 GenomeRNAi human phenotypes for PAMR1:
     Decreased cilium length after   Synthetic lethal with Ras 

    Animal Models:
         Mouse knock-out Pamr1tm1Lex for PAMR1
         1 MGI phenotypic allele for Pamr1 (no phenotypes)

    PAMR1 for phenotypes           About GeneDecksing


    (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 PAMR1

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006508proteolysis ----


    PAMR1 for ontologies           About GeneDecksing



    (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 PAMR1
    Search CenterWatch for drugs/clinical trials and news about PAMR1 

    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PAMR1 gene (2 alternative transcripts): 
    NM_001001991.1  NM_015430.2  

    Unigene Cluster for PAMR1:

    Peptidase domain containing associated with muscle regeneration 1
    Hs.55044  [show with all ESTs]
    Unigene Representative Sequence: BX640676
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000278360(uc001mwf.3) ENST00000378880(uc001mwg.3 uc010rew.2)
    ENST00000532848(uc010rex.2) ENST00000527605 ENST00000531219 ENST00000529303
    ENST00000534803 ENST00000378878

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    1 QIAGEN miScript miRNA Assays for microRNA that regulate PAMR1:
    hsa-miR-4318
    SwitchGear 3'UTR luciferase reporter plasmidPAMR1 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AF370388.1 AK027841.1 AK297092.1 AK300185.1 AK316188.1 AL050214.1 AL832391.1 AY358346.1 
    BC038457.1 BC089434.1 BX640676.1 

    3 DOTS entries:

    DT.99982487  DT.100751276  DT.75178838 

    24/75 AceView cDNA sequences (see all 75):

    AI420902 AA812954 BU742789 AY358346 BX399905 AA433935 BX282717 NM_015430 
    NM_001001991 AL701986 BQ694586 BE048236 CD514783 AI057206 AA460698 AI579963 
    AA989716 BG403264 AW069518 BQ014545 AW957662 AW028008 AA375185 BX439313 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for PAMR1    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13
    SP1:                                                  -                       -                           
    SP2:                                                  -     -                 -                           
    SP3:                                                                                                      
    SP4:                                                                                                      


    ECgene alternative splicing isoforms for PAMR1

    (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

    PAMR1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GCCACAGTAC

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

    About this image

    PAMR1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    10/26 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 26
    Tissue Anatomical Compartment CellCategory (developmental path)
    BoneSacral VertebraeOsteochondro Mesenchymal CellsBone, Cartilage
    CartilageCervical Intervertebral DiscIntervertebral Disc Annulus Fibrosus CellsCartilage
    CartilageCervical Intervertebral DiscIntervertebral Disc Nucleus Pulposus CellsCartilage
    LimbStylopod Synovial JointInterzone CellsCartilage
    OvaryPrimary FollicleGranulosa CellsOvary
    OvaryPrimordial FolliclePre-Granulosa CellsOvary
    BoneAutopod Long BoneBone
    BoneRostral Endochondral Facial BonesBone
    BoneRostral Skull Membranous BonesBone
    BrainMedulla OblongataBrain
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 7 LifeMap Cells 
    NameCategory
    PureStem™ myogenic progenitor Z11 (Embryonic Progenitor Cell)Heart, Myocardium, Smooth Muscle
    PureStem™ mesenchymal progenitor 7SMOO32 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor 7PEND24 (Embryonic Progenitor Cell)Cartilage, Neural Crest
    PureStem™ mesenchymal progenitor 4D20.8 (Embryonic Progenitor Cell)Lateral Plate Mesoderm, Neural Crest
    PureStem™ progenitor EN27 (Embryonic Progenitor Cell)
    PureStem™ progenitor W8 (Embryonic Progenitor Cell)
    PureStem™ progenitor Z1 (Embryonic Progenitor Cell)

    See PAMR1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PAMR1

    SOURCE GeneReport for Unigene cluster: Hs.55044
        SABiosciences Custom PCR Arrays for PAMR1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PAMR1

    (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 chordates.

    Orthologs for PAMR1 gene from 3/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves PAMR11 peptidase domain containing associated with muscle more 75.66(n)
    80.34(a)
      423158  XM_421084.3  XP_421084.2 
    lizard
    (Anolis carolinensis)
    Reptilia PAMR16
    --
    76(a)
    1 ↔ 1
    1(54550265-54652074)
    zebrafish
    (Danio rerio)
    Actinopterygii CU207301.136
    --
    49(a)
    1 ↔ 1
    25(38224190-38239458)


    ENSEMBL Gene Tree for PAMR1 (if available)
    TreeFam Gene Tree for PAMR1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PAMR1 gene
    PROZ2  C1S2  C1R2  C1RL2  F92  MASP12  F102  F22  
    HPR2  HP2  PROC2  F72  MASP22  
    5 SIMAP similar genes for PAMR1 using alignment to 5 protein entries:     PAMR1_HUMAN (see all proteins):
    MASP1    EGF    F9    SNED1    DKFZp586F0824

    PAMR1 for paralogs           About GeneDecksing



    (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

    10/88 NCBI SNPs in PAMR1 are shown (see all 88    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1995774381,2
    C--35453799(-) AACTTG/TGNNNN 1 -- ut310--------
    rs778516381,2
    C--35455317(+) TGGAT-/GGAT  
            
    AGACG
    1 -- int10--------
    rs744085611,2
    C,--35455318(+) TGGATA/GGACGG 1 -- int10--------
    rs349513131,2
    C--35458239(+) CACACAC/-TTTGC 2 -- int11Minor allele frequency- -:0.00NA 2
    rs1448557781,2
    C--35466939(+) AGTGA-/ATGAGA 2 -- int10--------
    rs573497891,2
    C--35467136(+) ATTTAGATA/-  
            
    ATCAT
    2 -- int11Minor allele frequency- -:0.00NA 2
    rs761545971,2
    C,--35500102(+) AGGGA-/GCTGCGCT 1 -- int10--------
    rs1849675411,2
    --35500136(+) TTCAAC/TTCCCT 1 -- int10--------
    rs802696371,2
    C,F,--35500154(+) CTTGCC/TTCTAC 1 -- int12Minor allele frequency- T:0.04WA EA 238
    rs5953341,2
    C,F,A,H,--35500292(-) TCTTTC/AAGACT 1 -- int15Minor allele frequency- A:0.01NS EA WA 534

    HapMap Linkage Disequilibrium report for PAMR1 (35453370 - 35551848 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for PAMR1
         3 CNVs: 3845 71308 71307

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PAMR1
    DNA2.0 Custom Variant and Variant Library Synthesis for PAMR1

    (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

    PAMR1 for disorders           About GeneDecksing

    3 diseases for PAMR1:    About MalaCards
    duchenne muscular dystrophy    muscular dystrophy    muscular atrophy

    Human Genome Epidemiology (HuGE) Navigator: PAMR1 (1 document)

    Export disorders for PAMR1 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 PAMR1 gene, integrated from 9 sources (see all 14):
    (articles sorted by number of sources associating them with PAMR1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning of cDNA encoding a regeneration-associated muscle protease whose expression is attenuated in cell lines derived from Duchenne muscular dystrophy patients. (PubMed id 15111323)1, 2, 3, 9 Nakayama Y.... Hara T. (2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (2003)
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    5. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    6. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PubMed id 16335952)2 Liu T.... Smith R.D. (2005)
    7. 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. (2004)
    8. Large-scale cDNA transfection screening for genes related to cancer development and progression. (PubMed id 15498874)2 Wan D....Gu J. (2004)
    9. 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)
    10. [Regenerative medicine of skeletal muscle] (PubMed id 16447752)9 Hara T....Nara N. (2005)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 25891 HGNC: 24554 AceView: DKFZP586H2123 Ensembl:ENSG00000149090 euGenes: HUgn25891
    ECgene: PAMR1 H-InvDB: PAMR1

    (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 PAMR1 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 PAMR1 gene:
    Search GeneIP for patents involving PAMR1

    GeneCards and IP:
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