Human Gene AGBL4 (ENST00000371839.6) from GENCODE V38
  Description: Homo sapiens ATP/GTP binding protein like 4 (AGBL4), transcript variant 5, non-coding RNA. (from RefSeq NR_136623)
Gencode Transcript: ENST00000371839.6
Gencode Gene: ENSG00000186094.17
Transcript (Including UTRs)
   Position: hg38 chr1:48,532,854-50,023,954 Size: 1,491,101 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg38 chr1:48,534,173-50,023,796 Size: 1,489,624 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2021-09-27 09:51:20

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:48,532,854-50,023,954)mRNA (may differ from genome)Protein (503 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaBioGPSCGAP
EnsemblEntrez GeneExonPrimerGeneCardsHGNCHPRD
LynxMGIneXtProtOMIMPubMedReactome
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CBPC6_HUMAN
DESCRIPTION: RecName: Full=Cytosolic carboxypeptidase 6; EC=3.4.17.-; AltName: Full=ATP/GTP-binding protein-like 4;
FUNCTION: Metallocarboxypeptidase that mediates deglutamylation of target proteins. Catalyzes the deglutamylation of polyglutamate side chains generated by post-translational polyglutamylation in proteins such as tubulins. Also removes gene-encoded polyglutamates from the carboxy-terminus of target proteins such as MYLK. Acts as a long-chain deglutamylase and specifically shortens long polyglutamate chains, while it is not able to remove the branching point glutamate, a process catalyzed by AGBL5/CCP5 (By similarity).
COFACTOR: Binds 1 zinc ion per subunit (By similarity).
SUBUNIT: Interacts with MYLK (By similarity).
SUBCELLULAR LOCATION: Cytoplasm, cytosol (By similarity).
SIMILARITY: Belongs to the peptidase M14 family.
SEQUENCE CAUTION: Sequence=BAG52938.1; Type=Frameshift; Positions=501; Sequence=BAG57648.1; Type=Frameshift; Positions=501;

-  MalaCards Disease Associations
  MalaCards Gene Search: AGBL4
Diseases sorted by gene-association score: macular degeneration, age-related, 1 (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.41 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 9.17 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -53.80158-0.341 Picture PostScript Text
3' UTR -378.201319-0.287 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000834 - Peptidase_M14

Pfam Domains:
PF00246 - Zinc carboxypeptidase

ModBase Predicted Comparative 3D Structure on Q5VU57
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsemblWormBase 
Protein SequenceProtein Sequence Protein SequenceProtein Sequence 
AlignmentAlignment AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004180 carboxypeptidase activity
GO:0004181 metallocarboxypeptidase activity
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
GO:0015631 tubulin binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006508 proteolysis
GO:0035608 protein deglutamylation
GO:0035609 C-terminal protein deglutamylation
GO:0035610 protein side chain deglutamylation
GO:0051607 defense response to virus

Cellular Component:
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005814 centriole
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0036064 ciliary basal body
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  AK094826 - Homo sapiens cDNA FLJ37507 fis, clone BRAWH2018206, weakly similar to Homo sapiens ATP/GTP binding protein-like 2 (AGBL2), mRNA.
AK294633 - Homo sapiens cDNA FLJ60499 complete cds.
AK294394 - Homo sapiens cDNA FLJ53507 complete cds, weakly similar to Homo sapiens ATP/GTP binding protein-like 2 (AGBL2), mRNA.
AK296221 - Homo sapiens cDNA FLJ56815 complete cds, weakly similar to Mus musculus ATP/GTP binding protein-like 3 (Agbl3), mRNA.
BC035739 - Homo sapiens ATP/GTP binding protein-like 4, mRNA (cDNA clone IMAGE:5741932), with apparent retained intron.
AK027348 - Homo sapiens cDNA FLJ14442 fis, clone HEMBB1001126.
BC144171 - Homo sapiens cDNA clone IMAGE:9052691.
BC126383 - Homo sapiens ATP/GTP binding protein-like 4, mRNA (cDNA clone MGC:161661 IMAGE:8992099), complete cds.
KJ903473 - Synthetic construct Homo sapiens clone ccsbBroadEn_12867 AGBL4 gene, encodes complete protein.
HQ258373 - Synthetic construct Homo sapiens clone IMAGE:100072802 Unknown protein gene, encodes complete protein.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q5VU57 (Reactome details) participates in the following event(s):

R-HSA-8866105 CCPs deglutamylate tubulin
R-HSA-8955332 Carboxyterminal post-translational modifications of tubulin
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B3KT26, B4DG37, CBPC6_HUMAN, CCP6, ENST00000371839.1, ENST00000371839.2, ENST00000371839.3, ENST00000371839.4, ENST00000371839.5, NR_136623, Q5VU57, uc001cru.1, uc001cru.2, uc001cru.3, uc001cru.4
UCSC ID: ENST00000371839.6
RefSeq Accession: NM_032785
Protein: Q5VU57 (aka CBPC6_HUMAN)
CCDS: CCDS44137.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.