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

Gene ID: 78933, updated on 21-Apr-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; nose; and trigeminal ganglion. Orthologous to human AGBL4 (AGBL carboxypeptidase 4). [provided by Alliance of Genome Resources, Apr 2022]
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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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
  • 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 (19) 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)

General gene information

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Markers

Homology

Clone Names

  • RP23-342E4.1

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables carboxypeptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
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 metallopeptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables peptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 
acts_upstream_of_or_within proteolysis IEA
Inferred from Electronic Annotation
more info
  
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 axon IGI
Inferred from Genetic Interaction
more info
 PubMed 
located_in cell projection IEA
Inferred from Electronic Annotation
more info
  
located_in centriole ISO
Inferred from Sequence Orthology
more info
  
located_in ciliary basal body ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
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
    Related
    ENSMUSP00000102202.2, ENSMUST00000106592.8
    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

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