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AGBL3 AGBL carboxypeptidase 3 [ Homo sapiens (human) ]

Gene ID: 340351, updated on 2-Nov-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, Nov 2024]
Expression
Broad expression in testis (RPKM 2.0), endometrium (RPKM 0.4) and 16 other tissues See more
Orthologs
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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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