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    AGBL4 AGBL carboxypeptidase 4 [ Homo sapiens (human) ]

    Gene ID: 84871, updated on 27-Nov-2024

    Summary

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    Official Symbol
    AGBL4provided by HGNC
    Official Full Name
    AGBL carboxypeptidase 4provided by HGNC
    Primary source
    HGNC:HGNC:25892
    See related
    Ensembl:ENSG00000186094 MIM:616476; AllianceGenome:HGNC:25892
    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
    CCP6
    Summary
    Predicted to enable metallocarboxypeptidase activity and tubulin binding activity. Predicted to be involved in C-terminal protein deglutamylation; defense response to virus; and protein side chain deglutamylation. Predicted to act upstream of or within several processes, including axonal transport of mitochondrion; positive regulation of ubiquitin-dependent protein catabolic process; and regulation of blastocyst development. Located in Golgi apparatus; centriole; and ciliary basal body. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
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    Genomic context

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    See AGBL4 in Genome Data Viewer
    Location:
    1p33
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (48522511..50023954, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (48393346..49902907, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (48998526..50489626, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene spermatogenesis associated 6 Neighboring gene uncharacterized LOC124904175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1010 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:48945175-48946016 Neighboring gene Sharpr-MPRA regulatory region 6906 Neighboring gene NANOG hESC enhancer GRCh37_chr1:48991897-48992398 Neighboring gene ribosomal protein L21 pseudogene 25 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:49110904-49111546 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:49111547-49112189 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:49152780-49153280 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:49174571-49174927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1011 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:49357925-49358617 Neighboring gene BEN domain containing 5 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:49471420-49472013 Neighboring gene uncharacterized LOC105378706 Neighboring gene uncharacterized LOC124904851 Neighboring gene AGBL4 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:49872569-49872784 Neighboring gene AGBL4 intronic transcript 1 Neighboring gene uncharacterized LOC107984954 Neighboring gene zinc finger protein 859, pseudogene Neighboring gene uncharacterized LOC105378708 Neighboring gene uncharacterized LOC105378709 Neighboring gene MT-ND2 pseudogene 29 Neighboring gene ELAV like RNA binding protein 4

    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. AGBL4 promotes malignant progression of glioblastoma via modulation of MMP-1 and inflammatory pathways. Zhang S, et al. Front Immunol, 2024. PMID 39007144, Free PMC Article
    2. CCP5 and CCP6 retain CP110 and negatively regulate ciliogenesis. Wang Y, et al. BMC Biol, 2023 May 24. PMID 37226238, Free PMC Article
    3. Comparison of the enzymatic and functional properties of three cytosolic carboxypeptidase family members. Wu HY, et al. J Biol Chem, 2015 Jan 9. PMID 25416787, Free PMC Article
    4. Clinical Relevance of Plasma DNA Methylation in Colorectal Cancer Patients Identified by Using a Genome-Wide High-Resolution Array. Lin PC, et al. Ann Surg Oncol, 2015 Dec. PMID 25472652
    5. Integrative mutation, haplotype and G × G interaction evidence connects ABGL4, LRP8 and PCSK9 genes to cardiometabolic risk. Guo T, et al. Sci Rep, 2016 Nov 17. PMID 27853278, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. AGBL4 promotes malignant progression of glioblastoma via modulation of MMP-1 and inflammatory pathways.
      Title: AGBL4 promotes malignant progression of glioblastoma via modulation of MMP-1 and inflammatory pathways.
    2. CCP5 and CCP6 retain CP110 and negatively regulate ciliogenesis.
      Title: CCP5 and CCP6 retain CP110 and negatively regulate ciliogenesis.
    3. Proximity Mapping of CCP6 Reveals Its Association with Centrosome Organization and Cilium Assembly.
      Title: Proximity Mapping of CCP6 Reveals Its Association with Centrosome Organization and Cilium Assembly.
    4. this is the first study to explore and validate the relationships between seven SNPs in the FAM65B, AGBL4, and CUX2 genes and ATDH in a Chinese population. On the basis of this case-control study, SNP rs10946737 in FAM65B may be associated with susceptibility to ATDH in Chinese Han anti-TB treatment patients.
      Title: Association of FAM65B, AGBL4, and CUX2 genetic polymorphisms with susceptibility to antituberculosis drug-induced hepatotoxicity: validation study in a Chinese Han population.
    5. ABGL4, LRP8 and PCSK9 polymorphisms and gene interactions increase cardiometabolic risk.
      Title: Integrative mutation, haplotype and G × G interaction evidence connects ABGL4, LRP8 and PCSK9 genes to cardiometabolic risk.
    6. AGBL4 promoter hypermethylation is associated with Colorectal Cancer.
      Title: Clinical Relevance of Plasma DNA Methylation in Colorectal Cancer Patients Identified by Using a Genome-Wide High-Resolution Array.
    7. Nna1 and CCP4 remove the C-terminal glutamate from substrates with two or more glutamates, whereas CCP6 requires four or more glutamates. CCP4 behaves as a promiscuous glutamase with little preference for chain length or neighboring amino acid composition
      Title: Comparison of the enzymatic and functional properties of three cytosolic carboxypeptidase family members.
    8. 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.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    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

    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

    Clone Names

    • FLJ14442

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metallocarboxypeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metallocarboxypeptidase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables tubulin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables tubulin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in C-terminal protein deglutamylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in anterograde axonal transport of mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in central nervous system neuron development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in defense response to virus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein deglutamylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein side chain deglutamylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of blastocyst development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde axonal transport of mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in axon cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centriole IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in ciliary basal body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    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 6
    Names
    ATP/GTP binding protein like 4
    protein deglutamylase CCP6
    NP_001310502.1
    NP_001310503.1
    NP_001310504.1
    NP_116174.3
    XP_011540610.1
    XP_011540612.1
    XP_016858084.1
    XP_016858085.1
    XP_016858087.1
    XP_054195235.1
    XP_054195236.1
    XP_054195237.1
    XP_054195238.1

    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_001323573.2 → NP_001310502.1  cytosolic carboxypeptidase 6 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC099788, AL355809, AL390023, AL391844, AL590432, AL591602, AL645507, AL645730
      UniProtKB/Swiss-Prot
      Q5VU57
      Conserved Domains (1) summary
      cd06908
      Location:190 → 450
      M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins

    2. NM_001323574.2 → NP_001310503.1  cytosolic carboxypeptidase 6 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC099788, AL355809, AL390023, AL391844, AL590432, AL591602, AL645507, AL645730

    3. NM_001323575.2 → NP_001310504.1  cytosolic carboxypeptidase 6 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC099788, AL355809, AL390023, AL391844, AL590432, AL591602, AL645507, AL645730
      Conserved Domains (2) summary
      cd06908
      Location:178 → 438
      M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins
      COG2866
      Location:48 → 450
      MpaA; Murein tripeptide amidase MpaA [Cell wall/membrane/envelope biogenesis]

    4. NM_032785.4 → NP_116174.3  cytosolic carboxypeptidase 6 isoform 1

      See identical proteins and their annotated locations for NP_116174.3

      Status: VALIDATED

      Source sequence(s)
      AC099788, AL355809, AL390023, AL391844, AL590432, AL591602, AL645507, AL645730
      Consensus CDS
      CCDS44137.1
      UniProtKB/Swiss-Prot
      B3KT26, B4DG37, Q5VU57
      Related
      ENSP00000360905.1, ENST00000371839.6
      Conserved Domains (2) summary
      cd06908
      Location:178 → 438
      M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins
      COG2866
      Location:48 → 450
      MpaA; Murein tripeptide amidase MpaA [Cell wall/membrane/envelope biogenesis]

    RNA

    1. NR_136623.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC097062, AC099788, AL355809, AL391844, AL590432, AL591602, AL645507, AL645730

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      48522511..50023954 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017002595.3 → XP_016858084.1  cytosolic carboxypeptidase 6 isoform X2

    2. XM_011542308.3 → XP_011540610.1  cytosolic carboxypeptidase 6 isoform X1

      Conserved Domains (1) summary
      cd06908
      Location:190 → 475
      M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins

    3. XM_017002596.3 → XP_016858085.1  cytosolic carboxypeptidase 6 isoform X3

    4. XM_017002598.3 → XP_016858087.1  cytosolic carboxypeptidase 6 isoform X5

      UniProtKB/TrEMBL
      B1ANV5

    5. XM_011542310.3 → XP_011540612.1  cytosolic carboxypeptidase 6 isoform X4

      Conserved Domains (1) summary
      cl11393
      Location:190 → 225
      Peptidase_M14_like; M14 family of metallocarboxypeptidases and related proteins

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      48393346..49902907 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339260.1 → XP_054195235.1  cytosolic carboxypeptidase 6 isoform X1

    2. XM_054339261.1 → XP_054195236.1  cytosolic carboxypeptidase 6 isoform X3

    3. XM_054339263.1 → XP_054195238.1  cytosolic carboxypeptidase 6 isoform X5

    4. XM_054339262.1 → XP_054195237.1  cytosolic carboxypeptidase 6 isoform X4

    RNA

    1. XR_008486185.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VU57.3 GenPept UniProtKB/Swiss-Prot:Q5VU57

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