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    Agbl4 ATP/GTP binding protein-like 4 [ Mus musculus (house mouse) ]

    Gene ID: 78933, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Agbl4provided by MGI
    Official Full Name
    ATP/GTP binding protein-like 4provided by MGI
    Primary source
    MGI:MGI:1918244
    See related
    Ensembl:ENSMUSG00000061298 AllianceGenome:MGI:1918244
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    4930578N11Rik; 4931433A01Rik
    Summary
    Enables metallocarboxypeptidase activity and tubulin binding activity. Involved in C-terminal protein deglutamylation; defense response to virus; and protein side chain deglutamylation. Acts 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 cytosol. Is expressed in brain; early embryo; nose; and trigeminal ganglion. Orthologous to human AGBL4 (AGBL carboxypeptidase 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis adult (RPKM 3.9), cortex adult (RPKM 0.7) and 3 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Agbl4 in Genome Data Viewer
    Location:
    4 C7- D1; 4 51.43 cM
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (110254823..111521521)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (110397649..111664324)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_11078 Neighboring gene STARR-seq mESC enhancer starr_11079 Neighboring gene predicted gene, 33070 Neighboring gene STARR-seq mESC enhancer starr_11080 Neighboring gene STARR-seq mESC enhancer starr_11081 Neighboring gene ELAV like RNA binding protein 4 Neighboring gene predicted gene, 54251 Neighboring gene STARR-seq mESC enhancer starr_11082 Neighboring gene STARR-seq mESC enhancer starr_11083 Neighboring gene predicted gene 12807 Neighboring gene STARR-seq mESC enhancer starr_11084 Neighboring gene STARR-seq mESC enhancer starr_11085 Neighboring gene STARR-seq mESC enhancer starr_11086 Neighboring gene STARR-seq mESC enhancer starr_11087 Neighboring gene STARR-positive B cell enhancer ABC_E2704 Neighboring gene STARR-seq mESC enhancer starr_11088 Neighboring gene microfibrillar-associated protein 1B pseudogene Neighboring gene crumbs homolog 1 pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E1278 Neighboring gene STARR-positive B cell enhancer ABC_E11250 Neighboring gene STARR-seq mESC enhancer starr_11089 Neighboring gene BEN domain containing 5 Neighboring gene STARR-seq mESC enhancer starr_11090 Neighboring gene STARR-seq mESC enhancer starr_11091 Neighboring gene STARR-seq mESC enhancer starr_11092 Neighboring gene STARR-positive B cell enhancer ABC_E4646 Neighboring gene predicted gene, 33192 Neighboring gene spermatogenesis associated 6 Neighboring gene predicted gene 12961

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Tubulin polyglutamylation is a general traffic-control mechanism in hippocampal neurons. Bodakuntla S, et al. J Cell Sci, 2020 Feb 13. PMID 31932508
    2. Cytosolic carboxypeptidase CCP6 is required for megakaryopoiesis by modulating Mad2 polyglutamylation. Ye B, et al. J Exp Med, 2014 Nov 17. PMID 25332286, Free PMC Article
    3. Excessive tubulin polyglutamylation causes neurodegeneration and perturbs neuronal transport. Magiera MM, et al. EMBO J, 2018 Dec 3. PMID 30420556, Free PMC Article
    4. A novel subfamily of mouse cytosolic carboxypeptidases. Kalinina E, et al. FASEB J, 2007 Mar. PMID 17244818
    5. IL-7Rα glutamylation and activation of transcription factor Sall3 promote group 3 ILC development. Liu B, et al. Nat Commun, 2017 Aug 10. PMID 28794449, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • RP23-342E4.1

    Gene Ontology Provided by MGI

    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 metallocarboxypeptidase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables metallocarboxypeptidase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tubulin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables tubulin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in C-terminal protein deglutamylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in C-terminal protein deglutamylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within anterograde axonal transport of mitochondrion IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within axonal transport IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within central nervous system neuron development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in defense response to virus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of cell population proliferation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within protein deglutamylation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within protein deglutamylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein deglutamylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein side chain deglutamylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein side chain deglutamylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of blastocyst development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within retrograde axonal transport of mitochondrion IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in axon cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centriole ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in centriole ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in ciliary basal body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary basal body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in ciliary basal body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    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
    protein deglutamylase CCP6
    NP_001041654.2
    NP_001271119.1
    NP_084507.1
    XP_011238954.1
    XP_011238955.1
    XP_011238956.1
    XP_011238958.1
    XP_011238959.1
    XP_011238960.1
    XP_036020452.1
    XP_036020453.1

    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_001048189.4 → NP_001041654.2  cytosolic carboxypeptidase 6 isoform 2

      See identical proteins and their annotated locations for NP_001041654.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an altenate splice site in the 3' coding region compared to variant 1. It encodes isoform 2, which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL627183, AL627347, AL627425, AL662829, AL669940, AL669959, AL669965, AL671895
      Consensus CDS
      CCDS51263.1
      UniProtKB/Swiss-Prot
      Q09LZ8
      Related
      ENSMUSP00000079568.7, ENSMUST00000080744.13
      Conserved Domains (2) summary
      cd06908
      Location:187 → 438
      M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins
      pfam18027
      Location:46 → 130
      Pepdidase_M14_N; Cytosolic carboxypeptidase N-terminal domain

    2. NM_001284190.2 → NP_001271119.1  cytosolic carboxypeptidase 6 isoform 3

      See identical proteins and their annotated locations for NP_001271119.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate 3' exon structure compared to variant 1. It encodes isoform 3, which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL627183, AL627347, AL627425, AL662829, AL669940, AL669959, AL669965, AL671895
      Consensus CDS
      CCDS71443.1
      UniProtKB/TrEMBL
      E4W7Y4
      Conserved Domains (2) summary
      cd06908
      Location:187 → 438
      M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins
      pfam18027
      Location:46 → 130
      Pepdidase_M14_N; Cytosolic carboxypeptidase N-terminal domain

    3. NM_030231.3 → NP_084507.1  cytosolic carboxypeptidase 6 isoform 1

      See identical proteins and their annotated locations for NP_084507.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL627183, AL627347, AL627425, AL662829, AL669940, AL669959, AL669965, AL671895
      Consensus CDS
      CCDS51264.1
      UniProtKB/Swiss-Prot
      A2A979, A6PWC5, A6PWC6, Q09LZ8, Q09LZ9
      Related
      ENSMUSP00000095533.3, ENSMUST00000097920.9
      Conserved Domains (1) summary
      cd06908
      Location:178 → 438
      M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000070.7 Reference GRCm39 C57BL/6J

      Range
      110254823..111521521
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036164560.1 → XP_036020453.1  cytosolic carboxypeptidase 6 isoform X8

      Conserved Domains (2) summary
      pfam18027
      Location:46 → 130
      Pepdidase_M14_N; Cytosolic carboxypeptidase N-terminal domain
      cl11393
      Location:187 → 211
      Peptidase_M14_like; M14 family of metallocarboxypeptidases and related proteins

    2. XM_011240657.4 → XP_011238959.1  cytosolic carboxypeptidase 6 isoform X6

      Conserved Domains (2) summary
      pfam18027
      Location:65 → 142
      Pepdidase_M14_N; Cytosolic carboxypeptidase N-terminal domain
      cl11393
      Location:199 → 223
      Peptidase_M14_like; M14 family of metallocarboxypeptidases and related proteins

    3. XM_011240658.4 → XP_011238960.1  cytosolic carboxypeptidase 6 isoform X7

      Conserved Domains (2) summary
      pfam18027
      Location:65 → 142
      Pepdidase_M14_N; Cytosolic carboxypeptidase N-terminal domain
      cl11393
      Location:199 → 223
      Peptidase_M14_like; M14 family of metallocarboxypeptidases and related proteins

    4. XM_011240653.4 → XP_011238955.1  cytosolic carboxypeptidase 6 isoform X2

      Conserved Domains (2) summary
      cd06908
      Location:199 → 450
      M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins
      pfam18027
      Location:65 → 142
      Pepdidase_M14_N; Cytosolic carboxypeptidase N-terminal domain

    5. XM_011240654.4 → XP_011238956.1  cytosolic carboxypeptidase 6 isoform X3

      Conserved Domains (2) summary
      cd06908
      Location:199 → 450
      M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins
      pfam18027
      Location:65 → 142
      Pepdidase_M14_N; Cytosolic carboxypeptidase N-terminal domain

    6. XM_011240652.4 → XP_011238954.1  cytosolic carboxypeptidase 6 isoform X1

      Conserved Domains (2) summary
      cd06908
      Location:199 → 450
      M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins
      pfam18027
      Location:65 → 142
      Pepdidase_M14_N; Cytosolic carboxypeptidase N-terminal domain

    7. XM_036164559.1 → XP_036020452.1  cytosolic carboxypeptidase 6 isoform X4

      Conserved Domains (1) summary
      cd06908
      Location:74 → 325
      M14_AGBL4_like; Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins

    8. XM_011240656.4 → XP_011238958.1  cytosolic carboxypeptidase 6 isoform X5

      Conserved Domains (1) summary
      cl11393
      Location:1 → 171
      Peptidase_M14_like; M14 family of metallocarboxypeptidases and related proteins
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q09LZ8.1 GenPept UniProtKB/Swiss-Prot:Q09LZ8

    Gene LinkOut

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

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