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    PAMR1 peptidase domain containing associated with muscle regeneration 1 [ Homo sapiens (human) ]

    Gene ID: 25891, updated on 27-Nov-2024

    Summary

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    Official Symbol
    PAMR1provided by HGNC
    Official Full Name
    peptidase domain containing associated with muscle regeneration 1provided by HGNC
    Primary source
    HGNC:HGNC:24554
    See related
    Ensembl:ENSG00000149090 AllianceGenome:HGNC:24554
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RAMP; FP938; DKFZP586H2123
    Summary
    Predicted to enable calcium ion binding activity and serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in endometrium (RPKM 38.4), placenta (RPKM 23.8) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PAMR1 in Genome Data Viewer
    Location:
    11p13
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (35431827..35530300, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (35570662..35669082, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (35453374..35551848, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr11:35316953-35317454 Neighboring gene SLC1A2 antisense RNA 1 Neighboring gene solute carrier family 1 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4623 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:35351933-35352492 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:35366234-35366761 Neighboring gene NANOG hESC enhancer GRCh37_chr11:35369348-35369849 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:35440751-35441251 Neighboring gene SLC1A2 antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3258 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3259 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:35639867-35640028 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3261 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:35640328-35640962 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:35640963-35641597 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:35650952-35652151 Neighboring gene NANOG hESC enhancer GRCh37_chr11:35676186-35676747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4625 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:35684511-35685011 Neighboring gene four-jointed box kinase 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21277 Neighboring gene tripartite motif containing 44 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4627 Neighboring gene OCT4 hESC enhancer GRCh37_chr11:35774016-35774517 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:35793100-35793607

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of novel epigenetically inactivated gene PAMR1 in breast carcinoma. Lo PH, et al. Oncol Rep, 2015 Jan. PMID 25370079
    2. Cloning of cDNA encoding a regeneration-associated muscle protease whose expression is attenuated in cell lines derived from Duchenne muscular dystrophy patients. Nakayama Y, et al. Am J Pathol, 2004 May. PMID 15111323, Free PMC Article
    3. Common variants in left/right asymmetry genes and pathways are associated with relative hand skill. Brandler WM, et al. PLoS Genet, 2013. PMID 24068947, Free PMC Article
    4. A genome-wide association study (GWAS) for bronchopulmonary dysplasia. Wang H, et al. Pediatrics, 2013 Aug. PMID 23897914, Free PMC Article
    5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PAMR1 is a putative tumor suppressor which is frequently inactivated by promoter hypermethylation in breast cancer tissues.
      Title: Identification of novel epigenetically inactivated gene PAMR1 in breast carcinoma.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. RAMP may play a role in the regeneration of skeletal muscle, and its down-regulation could be involved in the progression of Duchenne muscular dystrophy
      Title: Cloning of cDNA encoding a regeneration-associated muscle protease whose expression is attenuated in cell lines derived from Duchenne muscular dystrophy patients.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association study (GWAS) for bronchopulmonary dysplasia.
    EBI GWAS Catalog
    Common variants in left/right asymmetry genes and pathways are associated with relative hand skill.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    inactive serine protease PAMR1
    Names
    peptidase domain-containing protein associated with muscle regeneration 1
    regeneration associated muscle protease
    regeneration-associated muscle protease homolog

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001001991.3 → NP_001001991.1  inactive serine protease PAMR1 isoform b precursor

      See identical proteins and their annotated locations for NP_001001991.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      AY358346, BC089434, BX640676
      Consensus CDS
      CCDS31460.1
      UniProtKB/Swiss-Prot
      A8MQ58, B7ZA73, Q5EBL7, Q5JPI4, Q6N062, Q6UXH9, Q71RE9, Q96JW2, Q9Y432
      UniProtKB/TrEMBL
      B7Z4A8
      Related
      ENSP00000483703.1, ENST00000619888.5
      Conserved Domains (5) summary
      cd00033
      Location:280 → 343
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00020
      Location:461 → 715
      Tryp_SPc; Trypsin-like serine protease
      cd00041
      Location:128 → 234
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      cd00054
      Location:240 → 272
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00190
      Location:461 → 718
      Tryp_SPc; Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad ...

    2. NM_001282675.2 → NP_001269604.1  inactive serine protease PAMR1 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream in-frame translational start codon, and lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AK297092, AL354921, AY358346
      Consensus CDS
      CCDS60759.1
      UniProtKB/TrEMBL
      A0A087WXE9, B7Z4A8
      Related
      ENSP00000480961.1, ENST00000621476.4
      Conserved Domains (5) summary
      cd00033
      Location:240 → 303
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00020
      Location:421 → 675
      Tryp_SPc; Trypsin-like serine protease
      cd00041
      Location:88 → 194
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      cd00054
      Location:200 → 232
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00190
      Location:421 → 678
      Tryp_SPc; Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad ...

    3. NM_001282676.2 → NP_001269605.1  inactive serine protease PAMR1 isoform d precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks three internal exons, resulting in the loss of two in-frame segments in the central coding region, compared to variant 1. The encoded isoform (d) is shorter than isoform a.
      Source sequence(s)
      AK300185, AL354921, AY358346
      Consensus CDS
      CCDS60760.1
      UniProtKB/TrEMBL
      B7Z6E5
      Related
      ENSP00000479260.1, ENST00000615849.4
      Conserved Domains (4) summary
      cd00033
      Location:169 → 232
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      smart00020
      Location:350 → 604
      Tryp_SPc; Trypsin-like serine protease
      cd00054
      Location:129 → 161
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00190
      Location:350 → 607
      Tryp_SPc; Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad ...

    4. NM_015430.4 → NP_056245.2  inactive serine protease PAMR1 isoform a precursor

      See identical proteins and their annotated locations for NP_056245.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AY358346, BC089434
      Consensus CDS
      CCDS7898.1
      UniProtKB/TrEMBL
      B7Z4A8
      Related
      ENSP00000482899.1, ENST00000622144.4
      Conserved Domains (4) summary
      cd00033
      Location:297 → 360
      CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
      cd00041
      Location:128 → 234
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      cd00054
      Location:240 → 272
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00190
      Location:478 → 735
      Tryp_SPc; Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      35431827..35530300 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      35570662..35669082 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6UXH9.1 GenPept UniProtKB/Swiss-Prot:Q6UXH9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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