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

Gene ID: 25891, updated on 5-Mar-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, Apr 2022]
Expression
Biased expression in endometrium (RPKM 38.4), placenta (RPKM 23.8) and 13 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (35431827..35530300, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (35570662..35669082, complement)
105.20220307 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)

Genotypes

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_2023_10

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

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