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    AGBL3 AGBL carboxypeptidase 3 [ Homo sapiens (human) ]

    Gene ID: 340351, updated on 28-Oct-2024

    Summary

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    Official Symbol
    AGBL3provided by HGNC
    Official Full Name
    AGBL carboxypeptidase 3provided by HGNC
    Primary source
    HGNC:HGNC:27981
    See related
    Ensembl:ENSG00000146856 MIM:617346; AllianceGenome:HGNC:27981
    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
    CCP3
    Summary
    Enables metallocarboxypeptidase activity. Involved in protein side chain deglutamylation. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Broad expression in testis (RPKM 2.0), endometrium (RPKM 0.4) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See AGBL3 in Genome Data Viewer
    Location:
    7q33
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (134986508..135135778)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (136294285..136443620)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (134671259..134820530)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901750 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:134426881-134427534 Neighboring gene tubulin beta 3 class III pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:134469373-134469873 Neighboring gene caldesmon 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:134529756-134530955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26694 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18675 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:134622660-134622865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26695 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26696 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26697 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26701 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:134760279-134760886 Neighboring gene MPRA-validated peak6750 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26702 Neighboring gene cell cycle regulator of NHEJ Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18676 Neighboring gene RNF14 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26708 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26710 Neighboring gene transmembrane protein 140 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:134877948-134879147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26712 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:134888580-134888794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18677 Neighboring gene microRNA 6509 Neighboring gene WD repeat domain 91

    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 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. Nna1-like proteins are active metallocarboxypeptidases of a new and diverse M14 subfamily. Rodriguez de la Vega M, et al. FASEB J, 2007 Mar. PMID 17244817
    2. The cytosolic carboxypeptidases CCP2 and CCP3 catalyze posttranslational removal of acidic amino acids. Tort O, et al. Mol Biol Cell, 2014 Oct 1. PMID 25103237, Free PMC Article
    3. Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients. Kennedy RB, et al. Hum Genet, 2012 Sep. PMID 22610502, Free PMC Article
    4. The DNA sequence of human chromosome 7. Hillier LW, et al. Nature, 2003 Jul 10. PMID 12853948
    5. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    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
    Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
    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

    Clone Names

    • FLJ12983, MGC32955

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metallocarboxypeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metallocarboxypeptidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tubulin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in protein side chain deglutamylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein side chain deglutamylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in centriole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in microtubule cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    cytosolic carboxypeptidase 3
    Names
    ATP/GTP binding protein like 3
    protein deglutamylase CCP3

    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_001345850.1 → NP_001332779.1  cytosolic carboxypeptidase 3 isoform b

      Status: VALIDATED

      Source sequence(s)
      AC083862, AC083870, AC090497
      Conserved Domains (1) summary
      cl11393
      Location:2 → 71
      Peptidase_M14_like; M14 family of metallocarboxypeptidases and related proteins

    2. NM_001345851.1 → NP_001332780.1  cytosolic carboxypeptidase 3 isoform c

      Status: VALIDATED

      Source sequence(s)
      AC083862, AC083870, AC090497

    3. NM_001345852.1 → NP_001332781.1  cytosolic carboxypeptidase 3 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) encodes isoform d. Variants 4 and 5 both encode the same isoform (d).
      Source sequence(s)
      AC083862, AC083870, AC090497
      Conserved Domains (1) summary
      cl11393
      Location:2 → 71
      Peptidase_M14_like; M14 family of metallocarboxypeptidases and related proteins

    4. NM_001345853.1 → NP_001332782.1  cytosolic carboxypeptidase 3 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) encodes isoform d. Variants 4 and 5 both encode the same isoform (d).
      Source sequence(s)
      AC083862, AC083870, AC090497
      Conserved Domains (1) summary
      cl11393
      Location:2 → 71
      Peptidase_M14_like; M14 family of metallocarboxypeptidases and related proteins

    5. NM_001367811.1 → NP_001354740.1  cytosolic carboxypeptidase 3 isoform e

      Status: VALIDATED

      Source sequence(s)
      AC083870, AC090497

    6. NM_001367812.1 → NP_001354741.1  cytosolic carboxypeptidase 3 isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8), as well as variant 9, encodes isoform f.
      Source sequence(s)
      AC083870, AC090497
      Related
      ENST00000476700.5

    7. NM_001367813.1 → NP_001354742.1  cytosolic carboxypeptidase 3 isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9), as well as variant 8, encodes isoform f.
      Source sequence(s)
      AC083870, AC090497

    8. NM_001367814.1 → NP_001354743.1  cytosolic carboxypeptidase 3 isoform g

      Status: VALIDATED

      Source sequence(s)
      AC083862, AC083870, AC090497

    9. NM_001367815.1 → NP_001354744.1  cytosolic carboxypeptidase 3 isoform h

      Status: VALIDATED

      Source sequence(s)
      AC083870, AC090497

    10. NM_001367816.1 → NP_001354745.1  cytosolic carboxypeptidase 3 isoform i

      Status: VALIDATED

      Description
      Transcript Variant: This variant (12), as well as variants 13 and 14, encodes isoform i.
      Source sequence(s)
      AC083870, AC090497

    11. NM_001367817.1 → NP_001354746.1  cytosolic carboxypeptidase 3 isoform i

      Status: VALIDATED

      Description
      Transcript Variant: This variant (13), as well as variants 12 and 14, encodes isoform i.
      Source sequence(s)
      AC083870, AC090497

    12. NM_001367818.1 → NP_001354747.1  cytosolic carboxypeptidase 3 isoform i

      Status: VALIDATED

      Description
      Transcript Variant: This variant (14), as well as variants 12 and 13, encodes isoform i.
      Source sequence(s)
      AC083870, AC090497
      Related
      ENST00000494702.2

    13. NM_001367819.1 → NP_001354748.1  cytosolic carboxypeptidase 3 isoform j

      Status: VALIDATED

      Source sequence(s)
      AC083870, AC090497

    14. NM_178563.4 → NP_848658.3  cytosolic carboxypeptidase 3 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AA707617, AC083862, AC090497, AK302827
      Consensus CDS
      CCDS47718.1
      UniProtKB/Swiss-Prot
      B7Z827, Q8NEM8, Q9H965
      Related
      ENSP00000388275.2, ENST00000436302.6
      Conserved Domains (1) summary
      cd06907
      Location:310 → 570
      M14_AGBL2-3_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-2 and AGBL-3, and related proteins

    RNA

    1. NR_144293.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC083862, AC083870, AC090497

    2. NR_160297.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC083870, AC090497

    3. NR_160298.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC083870, AC090497

    4. NR_160299.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC083870
      Related
      ENST00000470839.1

    5. NR_160300.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC083862, AC083870, AC090497

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      134986508..135135778
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420319.1 → XP_047276275.1  cytosolic carboxypeptidase 3 isoform X2

    2. XM_047420318.1 → XP_047276274.1  cytosolic carboxypeptidase 3 isoform X1

      Related
      ENSP00000401220.2, ENST00000435976.6

    3. XM_047420320.1 → XP_047276276.1  cytosolic carboxypeptidase 3 isoform X3

      Related
      ENSP00000275763.6, ENST00000275763.10

    4. XM_047420322.1 → XP_047276278.1  cytosolic carboxypeptidase 3 isoform X5

    5. XM_047420321.1 → XP_047276277.1  cytosolic carboxypeptidase 3 isoform X4

    6. XM_011516122.4 → XP_011514424.1  cytosolic carboxypeptidase 3 isoform X6

      Conserved Domains (1) summary
      cl11393
      Location:310 → 502
      Peptidase_M14_like; M14 family of metallocarboxypeptidases and related proteins

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      136294285..136443620
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358107.1 → XP_054214082.1  cytosolic carboxypeptidase 3 isoform X2

    2. XM_054358106.1 → XP_054214081.1  cytosolic carboxypeptidase 3 isoform X1

    3. XM_054358108.1 → XP_054214083.1  cytosolic carboxypeptidase 3 isoform X3

    4. XM_054358110.1 → XP_054214085.1  cytosolic carboxypeptidase 3 isoform X5

    5. XM_054358109.1 → XP_054214084.1  cytosolic carboxypeptidase 3 isoform X4

    6. XM_054358111.1 → XP_054214086.1  cytosolic carboxypeptidase 3 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NEM8.2 GenPept UniProtKB/Swiss-Prot:Q8NEM8

    Gene LinkOut

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