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    TBC1D16 TBC1 domain family member 16 [ Homo sapiens (human) ]

    Gene ID: 125058, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TBC1D16provided by HGNC
    Official Full Name
    TBC1 domain family member 16provided by HGNC
    Primary source
    HGNC:HGNC:28356
    See related
    Ensembl:ENSG00000167291 MIM:616637; AllianceGenome:HGNC:28356
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Enables GTPase activator activity. Involved in regulation of receptor recycling. Located in cytosol and early endosome. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in fat (RPKM 12.8), kidney (RPKM 8.0) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TBC1D16 in Genome Data Viewer
    Location:
    17q25.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (79932343..80035872, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (80830270..80934528, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (77906142..78009671, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12922 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77809787-77810608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9092 Neighboring gene Sharpr-MPRA regulatory region 202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12923 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77811431-77812254 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77812255-77813076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77814721-77815544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77815545-77816366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9095 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:77824032-77825231 Neighboring gene chromobox 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12924 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:77842993-77843520 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:77843521-77844050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77862335-77862836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77875585-77876566 Neighboring gene long intergenic non-protein coding RNA 1979 Neighboring gene long intergenic non-protein coding RNA 1978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77917109-77917834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77917835-77918560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77921171-77921997 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77922367-77922950 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77923535-77924118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77922951-77923534 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77924703-77925286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77925287-77925870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77930057-77930557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77948310-77949214 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:77951994-77952173 Neighboring gene uncharacterized LOC124904073 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77961646-77962517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9097 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:77966696-77967895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77975818-77976678 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:77987013-77987179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77996703-77997568 Neighboring gene uncharacterized LOC124904072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78003463-78004332 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12927 Neighboring gene Sharpr-MPRA regulatory region 13982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78018463-78018964 Neighboring gene uncharacterized LOC124904074 Neighboring gene coiled-coil domain 40 molecular ruler complex subunit Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78039691-78040515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78056255-78056756 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78064021-78064580 Neighboring gene microRNA 1268b

    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. TBC1D16 predicts chemosensitivity and prognosis in adult acute myeloid leukemia (AML) patients. Liu H, et al. Eur J Pharmacol, 2021 Mar 15. PMID 33476656
    2. Expression of TBC1D16 Is Associated with Favorable Prognosis of Epithelial Ovarian Cancer. Yang Z, et al. Tohoku J Exp Med, 2018 Jul. PMID 29962380
    3. Novel Host Protein TBC1D16, a GTPase Activating Protein of Rab5C, Inhibits Prototype Foamy Virus Replication. Yan J, et al. Front Immunol, 2021. PMID 34367131, Free PMC Article
    4. An integrated approach to uncover drivers of cancer. Akavia UD, et al. Cell, 2010 Dec 10. PMID 21129771, Free PMC Article
    5. Characterisation of DNA methylation changes in EBF3 and TBC1D16 associated with tumour progression and metastasis in multiple cancer types. Rodger EJ, et al. Clin Epigenetics, 2019 Aug 5. PMID 31383000, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel Host Protein TBC1D16, a GTPase Activating Protein of Rab5C, Inhibits Prototype Foamy Virus Replication.
      Title: Novel Host Protein TBC1D16, a GTPase Activating Protein of Rab5C, Inhibits Prototype Foamy Virus Replication.
    2. TBC1D16 predicts chemosensitivity and prognosis in adult acute myeloid leukemia (AML) patients.
      Title: TBC1D16 predicts chemosensitivity and prognosis in adult acute myeloid leukemia (AML) patients.
    3. Findings suggest characteristic DNA methylation changes in TBC1D16 is relatively common tumor-associated epigenetic events in multiple tumor types, which is consistent with a potential role as more general drivers of tumor progression.
      Title: Characterisation of DNA methylation changes in EBF3 and TBC1D16 associated with tumour progression and metastasis in multiple cancer types.
    4. TBC1D16 is a predictive marker for favorable prognosis of Epithelial ovarian cancer.
      Title: Expression of TBC1D16 Is Associated with Favorable Prognosis of Epithelial Ovarian Cancer.
    5. Bipolar disorder participants with a history of Suicidal behavior showed less overall methylation in the intron 3 of TRE2/BUB2/CDC16 domain family member 16 (TBC1D16).
      Title: Investigation of correlations between DNA methylation, suicidal behavior and aging.
    6. RAB5C is identified as a new TBC1D16 target and showed that it regulates EGFR in melanoma cells.
      Title: Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR.
    7. TBC1D16 is a GTPase activating protein for Rab4A that regulates transferrin receptor recycling and EGFR trafficking and signaling.
      Title: TBC1D16 is a Rab4A GTPase activating protein that regulates receptor recycling and EGF receptor signaling.
    8. TBC1D16 and RAB27A, were identified known drivers of melanoma both are involved in the regulation of vesicular trafficking, which highlights this process as important for proliferation in melanoma.
      Title: An integrated approach to uncover drivers of cancer.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See Variation Viewer (GRCh37.p13)

    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

    • FLJ20748, MGC25062, DKFZp451F1311

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    NOT involved_in regulation of cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of receptor recycling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in early endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    TBC1 domain family member 16
    Names
    CTD-2529O21.1

    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_001271844.2 → NP_001258773.1  TBC1 domain family member 16 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains multiple differences in the 5' UTR and coding region, compared to variant 1, and initiates translation at an alternate start codon. The encoded isoform (b) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AC100791, BC062601
      Consensus CDS
      CCDS62353.1
      UniProtKB/Swiss-Prot
      Q8TBP0
      Related
      ENSP00000461522.1, ENST00000576768.5
      Conserved Domains (1) summary
      smart00164
      Location:58 → 277
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    2. NM_001271845.2 → NP_001258774.1  TBC1 domain family member 16 isoform c

      See identical proteins and their annotated locations for NP_001258774.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains multiple differences in the 5' UTR and coding region, compared to variant 1, and initiates translation at an alternate start codon. The encoded isoform (c) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AC100791, BC036947, BC062601
      Consensus CDS
      CCDS62351.1
      UniProtKB/Swiss-Prot
      Q8TBP0
      Related
      ENSP00000341517.7, ENST00000340848.11
      Conserved Domains (1) summary
      smart00164
      Location:62 → 290
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    3. NM_001271846.2 → NP_001258775.1  TBC1 domain family member 16 isoform d

      See identical proteins and their annotated locations for NP_001258775.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains multiple differences in both UTRs and the coding region, compared to variant 1, and initiates translation at an alternate start codon. The encoded isoform (d) is shorter and has distinct N- and C-termini, compared to isoform a.
      Source sequence(s)
      BC001525, BX092567, CR936670
      Consensus CDS
      CCDS62352.1
      UniProtKB/TrEMBL
      I3L0V9
      Related
      ENSP00000458766.1, ENST00000572862.5
      Conserved Domains (1) summary
      smart00164
      Location:62 → 272
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    4. NM_019020.4 → NP_061893.2  TBC1 domain family member 16 isoform a

      See identical proteins and their annotated locations for NP_061893.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC100791, AC116025, BC028290, BC062601, CN361974
      Consensus CDS
      CCDS11766.1
      UniProtKB/Swiss-Prot
      B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7
      Related
      ENSP00000309794.2, ENST00000310924.7
      Conserved Domains (1) summary
      smart00164
      Location:424 → 652
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      79932343..80035872 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435346.1 → XP_047291302.1  TBC1 domain family member 16 isoform X7

    2. XM_024450577.2 → XP_024306345.1  TBC1 domain family member 16 isoform X1

      Conserved Domains (1) summary
      smart00164
      Location:424 → 709
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    3. XM_024450579.2 → XP_024306347.1  TBC1 domain family member 16 isoform X2

      Conserved Domains (1) summary
      smart00164
      Location:423 → 708
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    4. XM_024450580.2 → XP_024306348.1  TBC1 domain family member 16 isoform X3

      Conserved Domains (1) summary
      smart00164
      Location:419 → 695
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    5. XM_047435356.1 → XP_047291312.1  TBC1 domain family member 16 isoform X19

    6. XM_047435354.1 → XP_047291310.1  TBC1 domain family member 16 isoform X18

    7. XM_047435351.1 → XP_047291307.1  TBC1 domain family member 16 isoform X15

    8. XM_047435350.1 → XP_047291306.1  TBC1 domain family member 16 isoform X14

    9. XM_047435357.1 → XP_047291313.1  TBC1 domain family member 16 isoform X20

    10. XM_047435353.1 → XP_047291309.1  TBC1 domain family member 16 isoform X17

    11. XM_047435359.1 → XP_047291315.1  TBC1 domain family member 16 isoform X22

    12. XM_047435352.1 → XP_047291308.1  TBC1 domain family member 16 isoform X16

    13. XM_047435358.1 → XP_047291314.1  TBC1 domain family member 16 isoform X21

    14. XM_017024187.2 → XP_016879676.1  TBC1 domain family member 16 isoform X12

      Conserved Domains (2) summary
      smart00164
      Location:200 → 428
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
      PRK12323
      Location:31 → 188
      PRK12323; DNA polymerase III subunit gamma/tau

    15. XM_047435349.1 → XP_047291305.1  TBC1 domain family member 16 isoform X13

    16. XM_047435348.1 → XP_047291304.1  TBC1 domain family member 16 isoform X11

    17. XM_024450582.2 → XP_024306350.1  TBC1 domain family member 16 isoform X23

      Conserved Domains (1) summary
      smart00164
      Location:53 → 338
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    18. XM_047435344.1 → XP_047291300.1  TBC1 domain family member 16 isoform X5

    19. XM_047435342.1 → XP_047291298.1  TBC1 domain family member 16 isoform X4

      UniProtKB/Swiss-Prot
      B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7

    20. XM_047435347.1 → XP_047291303.1  TBC1 domain family member 16 isoform X7

    21. XM_047435343.1 → XP_047291299.1  TBC1 domain family member 16 isoform X5

    22. XM_047435345.1 → XP_047291301.1  TBC1 domain family member 16 isoform X6

    23. XM_006721694.4 → XP_006721757.1  TBC1 domain family member 16 isoform X4

      See identical proteins and their annotated locations for XP_006721757.1

      UniProtKB/Swiss-Prot
      B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7
      Conserved Domains (1) summary
      smart00164
      Location:424 → 652
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    24. XM_024450578.2 → XP_024306346.1  TBC1 domain family member 16 isoform X1

      Conserved Domains (1) summary
      smart00164
      Location:424 → 709
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    25. XM_017024185.2 → XP_016879674.1  TBC1 domain family member 16 isoform X10

    26. XM_005257052.4 → XP_005257109.1  TBC1 domain family member 16 isoform X9

      Conserved Domains (1) summary
      smart00164
      Location:424 → 634
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    27. XM_024450581.2 → XP_024306349.1  TBC1 domain family member 16 isoform X8

      Conserved Domains (1) summary
      smart00164
      Location:424 → 691
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791802.1 Reference GRCh38.p14 PATCHES

      Range
      33071..58783 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      80830270..80934528 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315058.1 → XP_054171033.1  TBC1 domain family member 16 isoform X7

    2. XM_054315056.1 → XP_054171031.1  TBC1 domain family member 16 isoform X5

    3. XM_054315054.1 → XP_054171029.1  TBC1 domain family member 16 isoform X4

      UniProtKB/Swiss-Prot
      B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7

    4. XM_054315050.1 → XP_054171025.1  TBC1 domain family member 16 isoform X1

    5. XM_054315059.1 → XP_054171034.1  TBC1 domain family member 16 isoform X7

    6. XM_054315055.1 → XP_054171030.1  TBC1 domain family member 16 isoform X5

    7. XM_054315051.1 → XP_054171026.1  TBC1 domain family member 16 isoform X2

    8. XM_054315057.1 → XP_054171032.1  TBC1 domain family member 16 isoform X6

    9. XM_054315052.1 → XP_054171027.1  TBC1 domain family member 16 isoform X3

    10. XM_054315053.1 → XP_054171028.1  TBC1 domain family member 16 isoform X4

      UniProtKB/Swiss-Prot
      B9A6L7, I3L1E0, I3L4U2, Q8N3Z4, Q8TBP0, Q96DH7

    11. XM_054315049.1 → XP_054171024.1  TBC1 domain family member 16 isoform X1

    12. XM_054315071.1 → XP_054171046.1  TBC1 domain family member 16 isoform X19

    13. XM_054315070.1 → XP_054171045.1  TBC1 domain family member 16 isoform X18

    14. XM_054315067.1 → XP_054171042.1  TBC1 domain family member 16 isoform X15

    15. XM_054315066.1 → XP_054171041.1  TBC1 domain family member 16 isoform X14

    16. XM_054315072.1 → XP_054171047.1  TBC1 domain family member 16 isoform X20

    17. XM_054315069.1 → XP_054171044.1  TBC1 domain family member 16 isoform X17

    18. XM_054315068.1 → XP_054171043.1  TBC1 domain family member 16 isoform X16

    19. XM_054315074.1 → XP_054171049.1  TBC1 domain family member 16 isoform X22

    20. XM_054315073.1 → XP_054171048.1  TBC1 domain family member 16 isoform X21

    21. XM_054315064.1 → XP_054171039.1  TBC1 domain family member 16 isoform X12

    22. XM_054315063.1 → XP_054171038.1  TBC1 domain family member 16 isoform X11

    23. XM_054315065.1 → XP_054171040.1  TBC1 domain family member 16 isoform X13

    24. XM_054315062.1 → XP_054171037.1  TBC1 domain family member 16 isoform X10

    25. XM_054315061.1 → XP_054171036.1  TBC1 domain family member 16 isoform X9

    26. XM_054315060.1 → XP_054171035.1  TBC1 domain family member 16 isoform X8

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TBP0.1 GenPept UniProtKB/Swiss-Prot:Q8TBP0

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