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    TPGS2 tubulin polyglutamylase complex subunit 2 [ Homo sapiens (human) ]

    Gene ID: 25941, updated on 28-Oct-2024

    Summary

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    Official Symbol
    TPGS2provided by HGNC
    Official Full Name
    tubulin polyglutamylase complex subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:24561
    See related
    Ensembl:ENSG00000134779 MIM:620710; AllianceGenome:HGNC:24561
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    L17; PGs2; C18orf10; HMFN0601
    Summary
    This gene encodes a protein that is a component of the neuronal polyglutamylase complex, which plays a role in post-translational addition of glutamate residues to C-terminal tubulin tails. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2012]
    Expression
    Broad expression in testis (RPKM 16.4), brain (RPKM 5.6) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TPGS2 in Genome Data Viewer
    Location:
    18q12.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (36780024..36829002, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (36969322..37022119, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (34359987..34408965, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:33876522-33877499 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9404 Neighboring gene WDR45-like pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13236 Neighboring gene formin homology 2 domain containing 3 Neighboring gene MPRA-validated peak3117 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:34050630-34051186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13238 Neighboring gene MPRA-validated peak3119 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr18:34098259-34098446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:34098790-34099369 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:34099370-34099948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13240 Neighboring gene uncharacterized LOC105372071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13241 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:34254255-34254481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:34287179-34287680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13242 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:34349653-34349798 Neighboring gene NANOG hESC enhancer GRCh37_chr18:34367445-34367994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13243 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:34408535-34409327 Neighboring gene KIAA1328 Neighboring gene uncharacterized LOC105372069 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:34527890-34528524 Neighboring gene uncharacterized LOC124904287

    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 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. Suppression subtractive hybridization and expression profiling identifies a unique set of genes overexpressed in non-small-cell lung cancer. Petroziello J, et al. Oncogene, 2004 Oct 7. PMID 15334068
    2. Genome-wide association study of periodontal health measured by probing depth in adults ages 18-49 years. Shaffer JR, et al. G3 (Bethesda), 2014 Feb 19. PMID 24347629, Free PMC Article
    3. Tubulin polyglutamylase enzymes are members of the TTL domain protein family. Janke C, et al. Science, 2005 Jun 17. PMID 15890843
    4. Expression profiling and differential screening between hepatoblastomas and the corresponding normal livers: identification of high expression of the PLK1 oncogene as a poor-prognostic indicator of hepatoblastomas. Yamada S, et al. Oncogene, 2004 Aug 5. PMID 15221005
    5. Mapping the mammalian ribosome quality control complex interactome using proximity labeling approaches. Zuzow N, et al. Mol Biol Cell, 2018 May 15. PMID 29540532, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of periodontal health measured by probing depth in adults ages 18-49 years.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp586M1523

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein polyglutamylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in centriolar satellite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in microtubule IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    tubulin polyglutamylase complex subunit 2
    Names
    polyglutamylase subunit 2

    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_001271949.2 → NP_001258878.1  tubulin polyglutamylase complex subunit 2 isoform 2

      See identical proteins and their annotated locations for NP_001258878.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.
      Source sequence(s)
      AC009854, AC090333, AK295817, BX107606
      Consensus CDS
      CCDS62422.1
      UniProtKB/Swiss-Prot
      Q68CL5
      Related
      ENSP00000467392.1, ENST00000593035.5
      Conserved Domains (1) summary
      smart00860
      Location:44 → 157
      SMI1_KNR4; SMI1 / KNR4 family

    2. NM_001271950.2 → NP_001258879.1  tubulin polyglutamylase complex subunit 2 isoform 3

      See identical proteins and their annotated locations for NP_001258879.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region compared to variant 1. It encodes isoform 3 which is shorter than isoform 1.
      Source sequence(s)
      AB073382, AC009854, AC090333, BX107606
      Consensus CDS
      CCDS62421.1
      UniProtKB/Swiss-Prot
      Q68CL5
      Related
      ENSP00000372530.2, ENST00000383056.7
      Conserved Domains (1) summary
      smart00860
      Location:44 → 149
      SMI1_KNR4; SMI1 / KNR4 family

    3. NM_001271951.2 → NP_001258880.1  tubulin polyglutamylase complex subunit 2 isoform 4

      See identical proteins and their annotated locations for NP_001258880.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate 3' terminal exon compared to variant 1. It encodes isoform 4 which has a distinct and longer C-terminus compared to isoform 1.
      Source sequence(s)
      AC009854, AC090333, BG420782, BQ670058
      Consensus CDS
      CCDS62424.1
      UniProtKB/Swiss-Prot
      Q68CL5
      Related
      ENSP00000464780.1, ENST00000590842.5
      Conserved Domains (1) summary
      smart00860
      Location:44 → 192
      SMI1_KNR4; SMI1 / KNR4 family

    4. NM_001271952.2 → NP_001258881.1  tubulin polyglutamylase complex subunit 2 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains an alternate exon in the 5' coding region compared to variant 1 and its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR. These differences cause translation initiation at a downstream AUG and result in an isoform (5) which has a shorter N-terminus and a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC009854, BC022199, CX783476
      UniProtKB/TrEMBL
      K7ERK3
      Conserved Domains (1) summary
      smart00860
      Location:2 → 144
      SMI1_KNR4; SMI1 / KNR4 family

    5. NM_001271953.2 → NP_001258882.1  tubulin polyglutamylase complex subunit 2 isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate 3' terminal exon compared to variant 1. It encodes isoform 6 which has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AA677381, AC009854, AC090333, BU543495, CA425930
      UniProtKB/TrEMBL
      K7EP30
      Related
      ENSP00000468292.1, ENST00000591906.5
      Conserved Domains (1) summary
      smart00860
      Location:44 → 192
      SMI1_KNR4; SMI1 / KNR4 family

    6. NM_001271954.2 → NP_001258883.1  tubulin polyglutamylase complex subunit 2 isoform 7

      See identical proteins and their annotated locations for NP_001258883.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 3' coding region and the 3' UTR; its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR compared to variant 1. It encodes isoform 7 which has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC009854, BC022199
      Consensus CDS
      CCDS62423.1
      UniProtKB/TrEMBL
      K7EP30
      Related
      ENSP00000466973.1, ENST00000589049.5
      Conserved Domains (1) summary
      smart00860
      Location:44 → 192
      SMI1_KNR4; SMI1 / KNR4 family

    7. NM_001271955.2 → NP_001258884.1  tubulin polyglutamylase complex subunit 2 isoform 8

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) lacks three alternate exons in the 3' coding region and contains an alternate 3' terminal exon compared to variant 1. It encodes isoform 8 which has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC009854, AC090333, BG420782
      Consensus CDS
      CCDS74214.1
      UniProtKB/TrEMBL
      A0A087X1R7
      Related
      ENSP00000484407.1, ENST00000610723.4
      Conserved Domains (1) summary
      smart00860
      Location:44 → 84
      SMI1_KNR4; SMI1 / KNR4 family

    8. NM_001271956.2 → NP_001258885.1  tubulin polyglutamylase complex subunit 2 isoform 9

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) contains an alternate 3' terminal exon compared to variant 1. It encodes isoform 9 which has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC009854, AC090333, BM796279, DA512668
      Consensus CDS
      CCDS74215.1
      UniProtKB/TrEMBL
      A0A087WUC8, K7EP30
      Related
      ENSP00000478553.1, ENST00000614939.4
      Conserved Domains (1) summary
      smart00860
      Location:44 → 192
      SMI1_KNR4; SMI1 / KNR4 family

    9. NM_001330572.2 → NP_001317501.1  tubulin polyglutamylase complex subunit 2 isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC009854, AC090333
      Consensus CDS
      CCDS82248.1
      UniProtKB/TrEMBL
      K7EKC0, K7EP30
      Related
      ENSP00000465551.1, ENST00000587129.5

    10. NM_015476.4 → NP_056291.2  tubulin polyglutamylase complex subunit 2 isoform 1

      See identical proteins and their annotated locations for NP_056291.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1.
      Source sequence(s)
      AC009854, AC090333, BC015178, BX107606
      Consensus CDS
      CCDS32817.1
      UniProtKB/Swiss-Prot
      B4DIX2, K7EIJ9, Q4KN59, Q68CL5, Q8WTU3, Q96BT9, Q9Y435
      Related
      ENSP00000335144.3, ENST00000334295.9
      Conserved Domains (1) summary
      smart00860
      Location:44 → 192
      SMI1_KNR4; SMI1 / KNR4 family

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      36780024..36829002 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017025702.3 → XP_016881191.1  tubulin polyglutamylase complex subunit 2 isoform X4

    2. XM_017025701.3 → XP_016881190.1  tubulin polyglutamylase complex subunit 2 isoform X3

      UniProtKB/TrEMBL
      K7EP30
      Conserved Domains (1) summary
      smart00860
      Location:44 → 192
      SMI1_KNR4; SMI1 / KNR4 family

    3. XM_005258242.5 → XP_005258299.1  tubulin polyglutamylase complex subunit 2 isoform X1

      Conserved Domains (1) summary
      smart00860
      Location:44 → 149
      SMI1_KNR4; SMI1 / KNR4 family

    4. XM_011525917.4 → XP_011524219.1  tubulin polyglutamylase complex subunit 2 isoform X2

      Conserved Domains (1) summary
      smart00860
      Location:2 → 144
      SMI1_KNR4; SMI1 / KNR4 family

    RNA

    1. XR_007066143.1 RNA Sequence

    2. XR_007066142.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      36969322..37022119 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054318505.1 → XP_054174480.1  tubulin polyglutamylase complex subunit 2 isoform X3

    2. XM_054318506.1 → XP_054174481.1  tubulin polyglutamylase complex subunit 2 isoform X4

    3. XM_054318507.1 → XP_054174482.1  tubulin polyglutamylase complex subunit 2 isoform X5

    4. XM_054318503.1 → XP_054174478.1  tubulin polyglutamylase complex subunit 2 isoform X1

    5. XM_054318504.1 → XP_054174479.1  tubulin polyglutamylase complex subunit 2 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q68CL5.2 GenPept UniProtKB/Swiss-Prot:Q68CL5

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