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Aliases for AGBL5 Gene

Aliases for AGBL5 Gene

  • ATP/GTP Binding Protein Like 5 2 3 5
  • Cytosolic Carboxypeptidase 5 2 3
  • CCP5 3 4
  • Cytosolic Carboxypeptidase-Like Protein 5 3
  • ATP/GTP-Binding Protein-Like 5 4
  • EC 3.4.17.- 4
  • RP75 3

External Ids for AGBL5 Gene

Previous GeneCards Identifiers for AGBL5 Gene

  • GC02P027128
  • GC02P027265

Summaries for AGBL5 Gene

Entrez Gene Summary for AGBL5 Gene

  • This gene encodes a metallocarboxypeptidase involved in protein deglutamylation and a member of the peptidase M14 family of proteins. The encoded protein has been described as a "dual-functional" deglutamylase that can remove glutamate residues from both carboxyl termini and side chains of protein substrates. This deglutamylase activity may be important in antiviral immunity. Mutations in this gene are associated with retinitis pigmentosa. [provided by RefSeq, Jul 2016]

GeneCards Summary for AGBL5 Gene

AGBL5 (ATP/GTP Binding Protein Like 5) is a Protein Coding gene. Diseases associated with AGBL5 include Retinitis Pigmentosa 75 and Agbl5-Related Retinitis Pigmentosa. GO annotations related to this gene include tubulin binding and metallocarboxypeptidase activity. An important paralog of this gene is AGBL2.

UniProtKB/Swiss-Prot for AGBL5 Gene

  • Metallocarboxypeptidase that mediates protein deglutamylation. Specifically catalyzes the deglutamylation of the branching point glutamate side chains generated by post-translational glutamylation in proteins such as tubulins. In contrast, it is not able to act as a long-chain deglutamylase that shortens long polyglutamate chains, a process catalyzed by AGTPBP1/CCP1, AGBL2/CCP2, AGBL3/CCP3, AGBL1/CCP4 and AGBL4/CCP6. Mediates deglutamylation of CGAS/MB21D1, regulating the antiviral activity of CGAS/MB21D1.

Additional gene information for AGBL5 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for AGBL5 Gene

Genomics for AGBL5 Gene

Regulatory Elements for AGBL5 Gene

Enhancers for AGBL5 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02H027719 1.9 FANTOM5 Ensembl ENCODE dbSUPER 23.5 +678.4 678384 2 SIN3A GLI4 BRCA1 ZNF2 ZNF416 ATF7 FOS SP3 TSHZ1 ZNF623 SUPT7L CAD ZNF512 EIF2B4 GPN1 GTF3C2 ZNF513 AGBL5 GTF3C2-AS1 LOC105374363
GH02H026342 1.4 ENCODE dbSUPER 13.3 -696.6 -696595 6 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 CAD GTF3C2-AS1 ASXL2 ENSG00000272148 AGBL5 KIF3C GAREM2 ADGRF3 AGBL5-IT1 ENSG00000272056
GH02H027090 1.6 Ensembl ENCODE dbSUPER 10.4 +51.6 51552 6 FOXA2 MLX ZFP64 ARID4B DMAP1 YY1 SLC30A9 ZNF766 ZNF143 PAF1 KHK ABHD1 CGREF1 ATRAID SLC5A6 CAD PRR30 TCF23 PREB AGBL5-AS1
GH02H026784 1.1 ENCODE 13.3 -256.3 -256257 2 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZBTB7B PPM1G ASXL2 EIF2B4 ATRAID NRBP1 GPN1 GTF3C2 GTF3C2-AS1 CENPA AGBL5
GH02H026970 1.3 FANTOM5 ENCODE 10.6 -70.7 -70737 2 HDGF PKNOX1 ARID4B SIN3A ZNF143 ZNF207 ATF7 SP3 NCOA1 SREBF1 KHK LOC100129724 LOC105374337 AGBL5 AGBL5-AS1 DPYSL5 EMILIN1 SLC5A6 ATRAID MAPRE3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around AGBL5 on UCSC Golden Path with GeneCards custom track

Genomic Location for AGBL5 Gene

Chromosome:
2
Start:
27,042,364 bp from pter
End:
27,070,622 bp from pter
Size:
28,259 bases
Orientation:
Plus strand

Genomic View for AGBL5 Gene

Genes around AGBL5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
AGBL5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for AGBL5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for AGBL5 Gene

Proteins for AGBL5 Gene

  • Protein details for AGBL5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NDL9-CBPC5_HUMAN
    Recommended name:
    Cytosolic carboxypeptidase-like protein 5
    Protein Accession:
    Q8NDL9
    Secondary Accessions:
    • A2VDI7
    • B7WPG9
    • B7Z7I7
    • D6W548
    • Q53SW0
    • Q53SZ0
    • Q96IK8
    • Q9H6V0
    • Q9H8P8

    Protein attributes for AGBL5 Gene

    Size:
    886 amino acids
    Molecular mass:
    97534 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAX93164.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=AAY14655.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=BAB15151.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for AGBL5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for AGBL5 Gene

Post-translational modifications for AGBL5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for AGBL5 Gene

Domains & Families for AGBL5 Gene

Gene Families for AGBL5 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for AGBL5 Gene

Suggested Antigen Peptide Sequences for AGBL5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8NDL9

UniProtKB/Swiss-Prot:

CBPC5_HUMAN :
  • Belongs to the peptidase M14 family.
Family:
  • Belongs to the peptidase M14 family.
genes like me logo Genes that share domains with AGBL5: view

Function for AGBL5 Gene

Molecular function for AGBL5 Gene

UniProtKB/Swiss-Prot Function:
Metallocarboxypeptidase that mediates protein deglutamylation. Specifically catalyzes the deglutamylation of the branching point glutamate side chains generated by post-translational glutamylation in proteins such as tubulins. In contrast, it is not able to act as a long-chain deglutamylase that shortens long polyglutamate chains, a process catalyzed by AGTPBP1/CCP1, AGBL2/CCP2, AGBL3/CCP3, AGBL1/CCP4 and AGBL4/CCP6. Mediates deglutamylation of CGAS/MB21D1, regulating the antiviral activity of CGAS/MB21D1.

Enzyme Numbers (IUBMB) for AGBL5 Gene

Phenotypes From GWAS Catalog for AGBL5 Gene

Gene Ontology (GO) - Molecular Function for AGBL5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004181 metallocarboxypeptidase activity ISS --
GO:0008233 peptidase activity IEA --
GO:0008237 metallopeptidase activity IEA --
GO:0008270 zinc ion binding IEA --
GO:0015631 tubulin binding ISS,IEA --
genes like me logo Genes that share ontologies with AGBL5: view
genes like me logo Genes that share phenotypes with AGBL5: view

Human Phenotype Ontology for AGBL5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for AGBL5

CRISPR Products

miRNA for AGBL5 Gene

miRTarBase miRNAs that target AGBL5

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for AGBL5
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for AGBL5 Gene

Localization for AGBL5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for AGBL5 Gene

Cytoplasm, cytosol. Nucleus. Cytoplasm, cytoskeleton, spindle. Midbody. Note=Mainly cytoplasmic. Slight accumulation in the nucleus is observed (By similarity). Colocalizes with alpha-tubulin in the mitotic spindle and with midbody microtubules in the intercellular bridges formed during cytokinesis. {ECO:0000250 UniProtKB:Q09M02, ECO:0000269 PubMed:23085998}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for AGBL5 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for AGBL5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005737 cytoplasm IDA --
GO:0005819 spindle IEA --
GO:0005829 cytosol ISS --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with AGBL5: view

Pathways & Interactions for AGBL5 Gene

SuperPathways for AGBL5 Gene

No Data Available

Gene Ontology (GO) - Biological Process for AGBL5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0035608 protein deglutamylation ISS,IEA --
GO:0035611 protein branching point deglutamylation IEA,ISS --
GO:0051607 defense response to virus ISS,IEA --
genes like me logo Genes that share ontologies with AGBL5: view

No data available for Pathways by source and SIGNOR curated interactions for AGBL5 Gene

Drugs & Compounds for AGBL5 Gene

No Compound Related Data Available

Transcripts for AGBL5 Gene

Unigene Clusters for AGBL5 Gene

ATP/GTP binding protein-like 5:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for AGBL5
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for AGBL5 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b · 7c ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b · 11c ^ 12a · 12b ^ 13 ^ 14a · 14b ^
SP1: - - - - -
SP2: - -
SP3: - -
SP4: - - - -
SP5: - - - -
SP6: -
SP7:
SP8:
SP9: -

ExUns: 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21
SP1: - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8: -
SP9:

Relevant External Links for AGBL5 Gene

GeneLoc Exon Structure for
AGBL5
ECgene alternative splicing isoforms for
AGBL5

Expression for AGBL5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for AGBL5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for AGBL5 Gene

This gene is overexpressed in Testis (x12.4).

Protein differential expression in normal tissues from HIPED for AGBL5 Gene

This gene is overexpressed in Heart (67.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for AGBL5 Gene



Protein tissue co-expression partners for AGBL5 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of AGBL5 Gene:

AGBL5

SOURCE GeneReport for Unigene cluster for AGBL5 Gene:

Hs.138207

mRNA Expression by UniProt/SwissProt for AGBL5 Gene:

Q8NDL9-CBPC5_HUMAN
Tissue specificity: Expressed in brain.

Evidence on tissue expression from TISSUES for AGBL5 Gene

  • Skin(4.2)
  • Nervous system(3.2)
genes like me logo Genes that share expression patterns with AGBL5: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for AGBL5 Gene

Orthologs for AGBL5 Gene

This gene was present in the common ancestor of chordates.

Orthologs for AGBL5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia AGBL5 34 33
  • 99.66 (n)
OneToOne
cow
(Bos Taurus)
Mammalia AGBL5 33 34
  • 90.76 (n)
dog
(Canis familiaris)
Mammalia AGBL5 33 34
  • 90.29 (n)
mouse
(Mus musculus)
Mammalia Agbl5 33 16 34
  • 87.13 (n)
rat
(Rattus norvegicus)
Mammalia Agbl5 33
  • 86.07 (n)
oppossum
(Monodelphis domestica)
Mammalia AGBL5 34
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia AGBL5 34
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves AGBL5 34
  • 53 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia AGBL5 34
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia agbl5 33
  • 66.42 (n)
zebrafish
(Danio rerio)
Actinopterygii agbl5 33 34
  • 65.92 (n)
-- 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 56 (a)
OneToOne
Species where no ortholog for AGBL5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for AGBL5 Gene

ENSEMBL:
Gene Tree for AGBL5 (if available)
TreeFam:
Gene Tree for AGBL5 (if available)

Paralogs for AGBL5 Gene

Paralogs for AGBL5 Gene

genes like me logo Genes that share paralogs with AGBL5: view

Variants for AGBL5 Gene

Sequence variations from dbSNP and Humsavar for AGBL5 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs879253768 Pathogenic, Retinitis pigmentosa 75 (RP75) [MIM:617023] 27,055,228(+) ACCCC(A/G)ATGGT nc-transcript-variant, reference, missense
rs879253769 Pathogenic, Retinitis pigmentosa 75 (RP75) [MIM:617023] 27,055,171(+) ATCCC(C/T)GGGCC nc-transcript-variant, reference, missense
rs1000154584 -- 27,060,698(+) CCAGC(C/T)GTGAC intron-variant
rs1000202927 -- 27,054,851(+) CTCTA(A/G)CACCA intron-variant
rs1000209620 -- 27,060,696(+) TACCA(C/G)CTGTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for AGBL5 Gene

Variant ID Type Subtype PubMed ID
dgv6744n54 CNV loss 21841781
esv3590132 CNV loss 21293372
nsv455974 CNV loss 19166990
nsv817673 CNV gain 17921354
nsv833603 CNV loss 17160897

Variation tolerance for AGBL5 Gene

Residual Variation Intolerance Score: 11.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.40; 54.25% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for AGBL5 Gene

Human Gene Mutation Database (HGMD)
AGBL5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
AGBL5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for AGBL5 Gene

Disorders for AGBL5 Gene

MalaCards: The human disease database

(4) MalaCards diseases for AGBL5 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
retinitis pigmentosa 75
  • rp75
agbl5-related retinitis pigmentosa
  • retinitis pigmentosa 75
retinitis pigmentosa
  • retinitis pigmentosa 1
usher syndrome, type 1b
  • usher syndrome type 1
- elite association - COSMIC cancer census association via MalaCards
Search AGBL5 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CBPC5_HUMAN
  • Retinitis pigmentosa 75 (RP75) [MIM:617023]: A form of retinitis pigmentosa, a retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP75 inheritance is autosomal recessive. {ECO:0000269 PubMed:26355662, ECO:0000269 PubMed:26720455}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for AGBL5

Genetic Association Database (GAD)
AGBL5
Human Genome Epidemiology (HuGE) Navigator
AGBL5
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
AGBL5
genes like me logo Genes that share disorders with AGBL5: view

No data available for Genatlas for AGBL5 Gene

Publications for AGBL5 Gene

  1. Expanding the clinical, allelic, and locus heterogeneity of retinal dystrophies. (PMID: 26355662) Patel N … Alkuraya FS (Genetics in medicine : official journal of the American College of Medical Genetics 2016) 3 4 60
  2. Exome Sequencing Reveals AGBL5 as Novel Candidate Gene and Additional Variants for Retinitis Pigmentosa in Five Turkish Families. (PMID: 26720455) Kastner S … Epplen JT (Investigative ophthalmology & visual science 2015) 3 4 60
  3. Cytosolic carboxypeptidase 5 removes α- and γ-linked glutamates from tubulin. (PMID: 24022482) Berezniuk I … Fricker LD (The Journal of biological chemistry 2013) 2 3 60
  4. Functional segregation and emerging role of cilia-related cytosolic carboxypeptidases (CCPs). (PMID: 23085998) Rodríguez de la Vega Otazo M … Bautista JM (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2013) 3 4 60
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 45 60

Products for AGBL5 Gene

Sources for AGBL5 Gene

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