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    TNRC6C trinucleotide repeat containing adaptor 6C [ Homo sapiens (human) ]

    Gene ID: 57690, updated on 28-Oct-2024

    Summary

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    Official Symbol
    TNRC6Cprovided by HGNC
    Official Full Name
    trinucleotide repeat containing adaptor 6Cprovided by HGNC
    Primary source
    HGNC:HGNC:29318
    See related
    Ensembl:ENSG00000078687 MIM:610741; AllianceGenome:HGNC:29318
    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
    Predicted to enable RNA binding activity. Involved in miRNA-mediated post-transcriptional gene silencing; positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; and positive regulation of nuclear-transcribed mRNA poly(A) tail shortening. Predicted to be located in cytosol. Predicted to be active in P-body and nucleoplasm. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in brain (RPKM 4.2), testis (RPKM 3.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TNRC6C in Genome Data Viewer
    Location:
    17q25.3
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (77957557..78108835)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (78851592..79002521)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (75953639..76104916)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr17:75916395-75916599 Neighboring gene uncharacterized LOC105371909 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75925764-75926709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:75927682-75928293 Neighboring gene RNA, U1 small nuclear 80, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr17:75931085-75931586 Neighboring gene NANOG hESC enhancer GRCh37_chr17:75944811-75945341 Neighboring gene MPRA-validated peak3014 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9037 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:75954602-75955161 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:75955162-75955720 Neighboring gene RNA, U6 small nuclear 625, pseudogene Neighboring gene ubiquitin conjugating enzyme E2 V2 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12854 Neighboring gene CEB72 minisatellite repeat instability region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9039 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9043 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76129823-76130348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76130349-76130874 Neighboring gene transmembrane channel like 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76133293-76133934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76135219-76135858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12865 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9045 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:76137495-76138694 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12867 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76144923-76145422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76147835-76148412 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76148413-76148989 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12868 Neighboring gene transmembrane channel like 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76154005-76154506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12869 Neighboring gene chromosome 17 open reading frame 99 Neighboring gene eukaryotic translation initiation factor 5A pseudogene 2

    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. Early origin and adaptive evolution of the GW182 protein family, the key component of RNA silencing in animals. Zielezinski A, et al. RNA Biol, 2015. PMID 26106978, Free PMC Article
    2. Importance of the C-terminal domain of the human GW182 protein TNRC6C for translational repression. Zipprich JT, et al. RNA, 2009 May. PMID 19304925, Free PMC Article
    3. Massively parallel reporter assays discover de novo exonic splicing mutants in paralogs of Autism genes. Rhine CL, et al. PLoS Genet, 2022 Jan. PMID 35051175, Free PMC Article
    4. Structural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation. Jinek M, et al. Nat Struct Mol Biol, 2010 Feb. PMID 20098421, Free PMC Article
    5. Expression of TNRC6 (GW182) Proteins Is Not Necessary for Gene Silencing by Fully Complementary RNA Duplexes. Liu Z, et al. Nucleic Acid Ther, 2019 Dec. PMID 31670606, Free PMC Article

    See all (65) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Massively parallel reporter assays discover de novo exonic splicing mutants in paralogs of Autism genes.
      Title: Massively parallel reporter assays discover de novo exonic splicing mutants in paralogs of Autism genes.
    2. Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing.
      Title: Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing.
    3. Expression of TNRC6 (GW182) Proteins Is Not Necessary for Gene Silencing by Fully Complementary RNA Duplexes.
      Title: Expression of TNRC6 (GW182) Proteins Is Not Necessary for Gene Silencing by Fully Complementary RNA Duplexes.
    4. The TNRC6 proteins bind to the 5'end of HCV RNA in a miR-122-dependent fashion and contribute functionally to replication of the viral genome by spatially regulating binding of miR-122/Ago2 to the 5'UTR.
      Title: TNRC6 proteins modulate hepatitis C virus replication by spatially regulating the binding of miR-122/Ago2 complexes to viral RNA.
    5. confirmed the anti-proliferative, pro-apoptotic and pro-autophagy capabilities of TNRC6C-AS1 through STK4 methylation via the Hippo signalling pathway in thyroid carcinoma
      Title: Suppression of long non-coding RNA TNRC6C-AS1 protects against thyroid carcinoma through DNA demethylation of STK4 via the Hippo signalling pathway.
    6. These findings reveal that despite species-specific differences in the relative strength of the PABPC1-binding sites, the interaction between GW182 proteins and PABPC1 is critical for miRNA-mediated silencing in animal cells.
      Title: Two PABPC1-binding sites in GW182 proteins promote miRNA-mediated gene silencing.
    7. The authors show that a conserved motif in the human GW182 paralog TNRC6C interacts with the C-terminal domain of polyadenylate binding protein 1 (PABC) and present the crystal structure of the complex.
      Title: Structural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation.
    8. Our findings indicate that TNRC6C, is recruited to miRNA targets through an interaction between their N-terminal domain and an Argonaute protein
      Title: The C-terminal domains of human TNRC6A, TNRC6B, and TNRC6C silence bound transcripts independently of Argonaute proteins.
    9. Through deletion and mutagenesis, study identified the C-terminal part of TNRC6C encompassing the RRM RNA-binding motif as a key effector domain mediating protein synthesis repression by TNRC6C.
      Title: Importance of the C-terminal domain of the human GW182 protein TNRC6C for translational repression.
    Submit: New GeneRIF Correction

    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 analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
    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

    • FLJ20015, KIAA1582

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in miRNA-mediated gene silencing by inhibition of translation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in miRNA-mediated post-transcriptional gene silencing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in miRNA-mediated post-transcriptional gene silencing IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of nuclear-transcribed mRNA poly(A) tail shortening IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of nuclear-transcribed mRNA poly(A) tail shortening IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    trinucleotide repeat-containing gene 6C protein
    Names
    trinucleotide repeat containing 6C

    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_001142640.2 → NP_001136112.2  trinucleotide repeat-containing gene 6C protein isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC015804, AC021593
      UniProtKB/Swiss-Prot
      A0A8Q3SIH5, A0A8Q3SIS0, G3XAB8, Q86UE5, Q8N3D8, Q96MU9, Q9HCJ0
      UniProtKB/TrEMBL
      A0A1B0GU24
      Related
      ENSP00000512514.1, ENST00000696270.1
      Conserved Domains (4) summary
      smart00360
      Location:1762 → 1825
      RRM; RNA recognition motif
      cd14283
      Location:1148 → 1185
      UBA_TNR6C; UBA domain found in trinucleotide repeat-containing gene 6C protein (TNRC6C) and similar proteins
      pfam10427
      Location:1035 → 1151
      Ago_hook; Argonaute hook
      pfam12938
      Location:1227 → 1456
      M_domain; M domain of GW182

    2. NM_001395508.1 → NP_001382437.1  trinucleotide repeat-containing gene 6C protein isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC021593
      Consensus CDS
      CCDS45799.1
      UniProtKB/TrEMBL
      A0AAA9XYZ6
      Conserved Domains (6) summary
      cd14283
      Location:938 → 975
      UBA_TNR6C; UBA domain found in trinucleotide repeat-containing gene 6C protein (TNRC6C) and similar proteins
      pfam10427
      Location:825 → 941
      Ago_hook; Argonaute hook
      pfam12938
      Location:1017 → 1246
      M_domain; M domain of GW182
      pfam16608
      Location:1255 → 1548
      TNRC6-PABC_bdg; TNRC6-PABC binding domain
      cd12713
      Location:1544 → 1631
      RRM_TNRC6C; RNA recognition motif (RRM) found in vertebrate trinucleotide repeat-containing gene 6C protein (TNRC6C)
      NF033849
      Location:258 → 420
      ser_rich_anae_1; serine-rich protein

    3. NM_001395509.1 → NP_001382438.1  trinucleotide repeat-containing gene 6C protein isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC015804, AC021593
      UniProtKB/TrEMBL
      A0A1B0GU24
      Conserved Domains (4) summary
      smart00360
      Location:1731 → 1794
      RRM; RNA recognition motif
      cd14283
      Location:1148 → 1185
      UBA_TNR6C; UBA domain found in trinucleotide repeat-containing gene 6C protein (TNRC6C) and similar proteins
      pfam10427
      Location:1035 → 1151
      Ago_hook; Argonaute hook
      pfam12938
      Location:1236 → 1464
      M_domain; M domain of GW182

    4. NM_001395510.1 → NP_001382439.1  trinucleotide repeat-containing gene 6C protein isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC015804, AC021593
      Consensus CDS
      CCDS92403.1
      UniProtKB/TrEMBL
      A0A1B0GU24
      Related
      ENSP00000512702.1, ENST00000696541.1
      Conserved Domains (4) summary
      smart00360
      Location:1723 → 1786
      RRM; RNA recognition motif
      cd14283
      Location:1148 → 1185
      UBA_TNR6C; UBA domain found in trinucleotide repeat-containing gene 6C protein (TNRC6C) and similar proteins
      pfam10427
      Location:1035 → 1151
      Ago_hook; Argonaute hook
      pfam12938
      Location:1227 → 1456
      M_domain; M domain of GW182

    5. NM_001395511.1 → NP_001382440.1  trinucleotide repeat-containing gene 6C protein isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC021593
      UniProtKB/TrEMBL
      A0AAA9XYZ6
      Conserved Domains (4) summary
      smart00360
      Location:1560 → 1623
      RRM; RNA recognition motif
      cd14283
      Location:938 → 975
      UBA_TNR6C; UBA domain found in trinucleotide repeat-containing gene 6C protein (TNRC6C) and similar proteins
      pfam10427
      Location:825 → 941
      Ago_hook; Argonaute hook
      pfam12938
      Location:1026 → 1254
      M_domain; M domain of GW182

    6. NM_001395512.1 → NP_001382441.1  trinucleotide repeat-containing gene 6C protein isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC015804, AC021593
      UniProtKB/TrEMBL
      A0AAA9XYZ6
      Conserved Domains (6) summary
      cd14283
      Location:938 → 975
      UBA_TNR6C; UBA domain found in trinucleotide repeat-containing gene 6C protein (TNRC6C) and similar proteins
      pfam10427
      Location:825 → 941
      Ago_hook; Argonaute hook
      pfam12938
      Location:1017 → 1246
      M_domain; M domain of GW182
      pfam16608
      Location:1255 → 1509
      TNRC6-PABC_bdg; TNRC6-PABC binding domain
      cd12713
      Location:1505 → 1592
      RRM_TNRC6C; RNA recognition motif (RRM) found in vertebrate trinucleotide repeat-containing gene 6C protein (TNRC6C)
      NF033849
      Location:258 → 420
      ser_rich_anae_1; serine-rich protein

    7. NM_018996.3 → NP_061869.2  trinucleotide repeat-containing gene 6C protein isoform 2

      See identical proteins and their annotated locations for NP_061869.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (2) has the same N- and C-termini but lacks a 3 amino acid segment near the N-terminus and a 39 amino acid segment near the C-terminus, compared to isoform 1.
      Source sequence(s)
      AB046802, AC021593, AI337097, DA339992, DV080590
      UniProtKB/TrEMBL
      A0AAA9XYZ6
      Related
      ENSP00000468647.2, ENST00000588061.6
      Conserved Domains (5) summary
      cd12713
      Location:1513 → 1595
      RRM_TNRC6C; RNA recognition motif in vertebrate trinucleotide repeat-containing gene 6C protein (TNRC6C)
      cd14283
      Location:941 → 978
      UBA_TNR6C; UBA domain found in trinucleotide repeat-containing gene 6C protein (TNRC6C) and similar proteins
      pfam10427
      Location:822 → 938
      Ago_hook; Argonaute hook
      pfam12938
      Location:1020 → 1248
      M_domain; M domain of GW182
      pfam16608
      Location:1258 → 1512
      TNRC6-PABC_bdg; TNRC6-PABC binding domain

    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
      77957557..78108835
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047436496.1 → XP_047292452.1  trinucleotide repeat-containing gene 6C protein isoform X14

    2. XM_047436485.1 → XP_047292441.1  trinucleotide repeat-containing gene 6C protein isoform X1

    3. XM_006721996.5 → XP_006722059.4  trinucleotide repeat-containing gene 6C protein isoform X3

    4. XM_047436487.1 → XP_047292443.1  trinucleotide repeat-containing gene 6C protein isoform X4

    5. XM_006721997.5 → XP_006722060.4  trinucleotide repeat-containing gene 6C protein isoform X6

    6. XM_047436490.1 → XP_047292446.1  trinucleotide repeat-containing gene 6C protein isoform X8

    7. XM_047436492.1 → XP_047292448.1  trinucleotide repeat-containing gene 6C protein isoform X10

    8. XM_047436494.1 → XP_047292450.1  trinucleotide repeat-containing gene 6C protein isoform X12

    9. XM_047436486.1 → XP_047292442.1  trinucleotide repeat-containing gene 6C protein isoform X2

    10. XM_047436488.1 → XP_047292444.1  trinucleotide repeat-containing gene 6C protein isoform X5

    11. XM_047436489.1 → XP_047292445.1  trinucleotide repeat-containing gene 6C protein isoform X7

    12. XM_047436491.1 → XP_047292447.1  trinucleotide repeat-containing gene 6C protein isoform X9

    13. XM_047436493.1 → XP_047292449.1  trinucleotide repeat-containing gene 6C protein isoform X11

    14. XM_047436495.1 → XP_047292451.1  trinucleotide repeat-containing gene 6C protein isoform X13

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      78851592..79002521
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316816.1 → XP_054172791.1  trinucleotide repeat-containing gene 6C protein isoform X14

    2. XM_054316803.1 → XP_054172778.1  trinucleotide repeat-containing gene 6C protein isoform X1

    3. XM_054316805.1 → XP_054172780.1  trinucleotide repeat-containing gene 6C protein isoform X3

    4. XM_054316806.1 → XP_054172781.1  trinucleotide repeat-containing gene 6C protein isoform X4

    5. XM_054316808.1 → XP_054172783.1  trinucleotide repeat-containing gene 6C protein isoform X6

    6. XM_054316810.1 → XP_054172785.1  trinucleotide repeat-containing gene 6C protein isoform X8

    7. XM_054316812.1 → XP_054172787.1  trinucleotide repeat-containing gene 6C protein isoform X10

    8. XM_054316814.1 → XP_054172789.1  trinucleotide repeat-containing gene 6C protein isoform X12

    9. XM_054316804.1 → XP_054172779.1  trinucleotide repeat-containing gene 6C protein isoform X2

    10. XM_054316807.1 → XP_054172782.1  trinucleotide repeat-containing gene 6C protein isoform X5

    11. XM_054316809.1 → XP_054172784.1  trinucleotide repeat-containing gene 6C protein isoform X7

    12. XM_054316811.1 → XP_054172786.1  trinucleotide repeat-containing gene 6C protein isoform X9

    13. XM_054316813.1 → XP_054172788.1  trinucleotide repeat-containing gene 6C protein isoform X11

    14. XM_054316815.1 → XP_054172790.1  trinucleotide repeat-containing gene 6C protein isoform X13

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HCJ0.4 GenPept UniProtKB/Swiss-Prot:Q9HCJ0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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