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    UBE3B ubiquitin protein ligase E3B [ Homo sapiens (human) ]

    Gene ID: 89910, updated on 3-Apr-2024

    Summary

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    Official Symbol
    UBE3Bprovided by HGNC
    Official Full Name
    ubiquitin protein ligase E3Bprovided by HGNC
    Primary source
    HGNC:HGNC:13478
    See related
    Ensembl:ENSG00000151148 MIM:608047; AllianceGenome:HGNC:13478
    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
    KOS; BPIDS
    Summary
    The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes, and E3 ubiquitin-protein ligases. This gene encodes a member of the E3 ubiquitin-conjugating enzyme family which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme and transfers the ubiquitin to the targeted substrates. A HECT (homology to E6-AP C-terminus) domain in the C-terminus of the longer isoform of this protein is the catalytic site of ubiquitin transfer and forms a complex with E2 conjugases. Shorter isoforms of this protein which lack the C-terminal HECT domain are therefore unlikely to bind E2 enzymes. Alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2012]
    Expression
    Ubiquitous expression in thyroid (RPKM 7.7), testis (RPKM 7.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    12q24.11
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (109477634..109547829)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (109452543..109519796)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (109915439..109974507)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene myosin IH Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6985 Neighboring gene long intergenic non-protein coding RNA 1486 Neighboring gene MPRA-validated peak1943 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109871570-109872074 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109896331-109897136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109897944-109898749 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109898750-109899556 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109900363-109901169 Neighboring gene potassium channel tetramerization domain containing 10 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:109914018-109914753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109976965-109977466 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109978915-109979477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109995443-109995944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109999353-109999852 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110001138-110001638 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110010699-110011200 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110011201-110011700 Neighboring gene RNA, U4 small nuclear 32, pseudogene Neighboring gene metabolism of cobalamin associated B Neighboring gene mevalonate kinase

    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
    • 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. Blepharophimosis-ptosis-intellectual disability syndrome: A report of nine Egyptian patients with further expansion of phenotypic and mutational spectrum. Zaki MS, et al. Am J Med Genet A, 2020 Dec. PMID 32949109
    2. Kaufman oculocerebrofacial syndrome: Novel UBE3B mutations and clinical features in four unrelated patients. Yilmaz R, et al. Am J Med Genet A, 2018 Jan. PMID 29160006
    3. Kaufman oculo-cerebro-facial syndrome in a child with small and absent terminal phalanges and absent nails. Kariminejad A, et al. J Hum Genet, 2017 Apr. PMID 28003643, Free PMC Article
    4. Kaufman Oculocerebrofacial Syndrome. Adam MP, et al. , 1993. PMID 27763745
    5. Kaufman oculocerebrofacial syndrome in sisters with novel compound heterozygous mutation in UBE3B. Pedurupillay CR, et al. Am J Med Genet A, 2015 Mar. PMID 25691420

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel UBE3B mutations: report of eight patients with Kaufman oculocerebrofacial syndrome with additional clinical findings from a highly consanguineous population.
      Title: Novel UBE3B mutations: report of eight patients with Kaufman oculocerebrofacial syndrome with additional clinical findings from a highly consanguineous population.
    2. UBE3B promotes breast cancer progression by antagonizing HIF-2alpha degradation.
      Title: UBE3B promotes breast cancer progression by antagonizing HIF-2α degradation.
    3. Blepharophimosis-ptosis-intellectual disability syndrome: A report of nine Egyptian patients with further expansion of phenotypic and mutational spectrum.
      Title: Blepharophimosis-ptosis-intellectual disability syndrome: A report of nine Egyptian patients with further expansion of phenotypic and mutational spectrum.
    4. TRIB3 promotes MYC-associated lymphoma development through suppression of UBE3B-mediated MYC degradation.
      Title: TRIB3 promotes MYC-associated lymphoma development through suppression of UBE3B-mediated MYC degradation.
    5. we present four patients with five novel UBE3B mutations and propose the inclusion of clinical features to the characteristics of Kaufman oculocerebrofacial syndrome, including prominence of the cheeks and limb anomalies.
      Title: Kaufman oculocerebrofacial syndrome: Novel UBE3B mutations and clinical features in four unrelated patients.
    6. studies demonstrate that UBE3B is an E3 ubiquitin ligase and reveal that the enzyme is regulated by calmodulin. Furthermore, the modulation of UBE3B via calmodulin and calcium implicates a role for calcium signaling in mitochondrial protein ubiquitylation, protein turnover, and disease
      Title: UBE3B Is a Calmodulin-regulated, Mitochondrion-associated E3 Ubiquitin Ligase.
    7. Sanger sequencing was negative for the DOORS syndrome gene TBC1D24 but exome sequencing identified a homozygous deletion in UBE3B (NM_183415:c.3139_3141del, p.1047_1047del) located within the terminal portion of the HECT domain
      Title: Kaufman oculo-cerebro-facial syndrome in a child with small and absent terminal phalanges and absent nails.
    8. The E3 ligase activity of UBE3B is regulated by its interaction with calmodulin via the N-terminal IQ domain.
      Title: UBE3B Is a Calmodulin-regulated, Mitochondrion-associated E3 Ubiquitin Ligase.
    9. UBE3B encodes a widely expressed protein ubiquitin ligase E3B, which, when mutated in both alleles, causes Kaufman oculocerebrofacial syndrome.
      Title: Kaufman oculocerebrofacial syndrome in sisters with novel compound heterozygous mutation in UBE3B.
    10. UBE3B mutations cause a clinically recognizable and possibly underdiagnosed syndrome named the Kaufman oculocerebrofacial syndrome
      Title: Expanding the clinical and mutational spectrum of Kaufman oculocerebrofacial syndrome with biallelic UBE3B mutations.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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

    Associated conditions

    Description Tests
    Oculocerebrofacial syndrome, Kaufman type
    MedGen: C1855663 OMIM: 244450 GeneReviews: Kaufman Oculocerebrofacial Syndrome
    		Compare labs

    EBI GWAS Catalog

    Description
    Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ45294, MGC78388, MGC131858, DKFZp586K2123, DKFZp686A1051

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in protein polyubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin-protein ligase E3B
    Names
    HECT-type ubiquitin transferase E3B
    NP_001257378.1
    NP_001257379.1
    NP_001257380.1
    NP_569733.2
    NP_904324.1
    XP_005254044.1
    XP_006719744.1
    XP_006719745.1
    XP_011537261.1
    XP_011537263.1
    XP_016875685.1
    XP_047285800.1
    XP_047285801.1
    XP_047285802.1
    XP_047285803.1
    XP_047285804.1
    XP_047285805.1
    XP_047285806.1
    XP_047285807.1
    XP_047285808.1
    XP_047285809.1
    XP_047285810.1
    XP_054229740.1
    XP_054229741.1
    XP_054229742.1
    XP_054229743.1
    XP_054229744.1
    XP_054229745.1
    XP_054229746.1
    XP_054229747.1
    XP_054229748.1
    XP_054229749.1
    XP_054229750.1
    XP_054229751.1
    XP_054229752.1
    XP_054229753.1
    XP_054229754.1
    XP_054229755.1
    XP_054229756.1

    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.

    Genomic

    1. NG_033898.2 RefSeqGene

      Range
      5002..64070
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001270449.2 → NP_001257378.1  ubiquitin-protein ligase E3B isoform 3

      See identical proteins and their annotated locations for NP_001257378.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate 3' exon, compared to variant 1. This difference results in a distinct 3' UTR and 3' coding region and a protein (isoform 3) with a shorter and distinct C-terminus, compared to isoform 1. Variants 4-6 encode the same protein (isoform 3).
      Source sequence(s)
      BC051266, DA771082
      Consensus CDS
      CCDS58277.1
      UniProtKB/TrEMBL
      F5H6D6
      Related
      ENSP00000342614.5, ENST00000340074.9

    2. NM_001270450.2 → NP_001257379.1  ubiquitin-protein ligase E3B isoform 3

      See identical proteins and their annotated locations for NP_001257379.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in the 5' UTR and contains an alternate 3' exon, compared to variant 1. These differences result in a distinct 3' UTR and 3' coding region and a protein (isoform 3) with a shorter and distinct C-terminus, compared to isoform 1. Variants 4-6 encode the same protein (isoform 3).
      Source sequence(s)
      BC108705, DA771082
      Consensus CDS
      CCDS58277.1
      UniProtKB/TrEMBL
      F5H6D6
      Related
      ENSP00000440585.1, ENST00000536398.5
      Conserved Domains (1) summary
      cl15479
      Location:30 → 50
      IQ; IQ calmodulin-binding motif

    3. NM_001270451.2 → NP_001257380.1  ubiquitin-protein ligase E3B isoform 3

      See identical proteins and their annotated locations for NP_001257380.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate splice site in the 5' UTR and contains an alternate 3' exon, compared to variant 1. These differences result in a distinct 3' UTR and 3' coding region and a protein (isoform 3) with a shorter and distinct C-terminus, compared to isoform 1. Variants 4-6 encode the same protein (isoform 3).
      Source sequence(s)
      BC068221, BC108705, DA771082
      Consensus CDS
      CCDS58277.1
      UniProtKB/TrEMBL
      F5H6D6
      Related
      ENSP00000443565.1, ENST00000540230.5
      Conserved Domains (1) summary
      cl15479
      Location:30 → 50
      IQ; IQ calmodulin-binding motif

    4. NM_130466.4 → NP_569733.2  ubiquitin-protein ligase E3B isoform 1

      See identical proteins and their annotated locations for NP_569733.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript, and encodes the longer protein (isoform 1). Variants 1 and 3 encode the same protein (isoform 1).
      Source sequence(s)
      AF251046, BC032301, BC144684, BQ889238, DA771082, DR760197
      Consensus CDS
      CCDS9129.1
      UniProtKB/Swiss-Prot
      A5D8Z3, Q05BX9, Q659F7, Q7Z3V4, Q7Z7Q1, Q9BXZ4
      UniProtKB/TrEMBL
      B9EK57
      Related
      ENSP00000340596.3, ENST00000342494.8
      Conserved Domains (1) summary
      cd00078
      Location:682 → 1066
      HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...

    5. NM_183415.3 → NP_904324.1  ubiquitin-protein ligase E3B isoform 1

      See identical proteins and their annotated locations for NP_904324.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR, as compared to variant 1. Variants 1 and 3 encode the same protein (isoform 1).
      Source sequence(s)
      AF251046, BC032301, BQ889238, DA771082, DR760197
      Consensus CDS
      CCDS9129.1
      UniProtKB/Swiss-Prot
      A5D8Z3, Q05BX9, Q659F7, Q7Z3V4, Q7Z7Q1, Q9BXZ4
      UniProtKB/TrEMBL
      B9EK57
      Related
      ENSP00000391529.2, ENST00000434735.6
      Conserved Domains (1) summary
      cd00078
      Location:682 → 1066
      HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      109477634..109547829
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011538961.2 → XP_011537263.1  ubiquitin-protein ligase E3B isoform X5

      UniProtKB/TrEMBL
      B9EK57
      Conserved Domains (1) summary
      cd00078
      Location:682 → 1007
      HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...

    2. XM_047429852.1 → XP_047285808.1  ubiquitin-protein ligase E3B isoform X5

    3. XM_047429851.1 → XP_047285807.1  ubiquitin-protein ligase E3B isoform X5

    4. XM_047429853.1 → XP_047285809.1  ubiquitin-protein ligase E3B isoform X6

      Related
      ENSP00000443131.1, ENST00000539599.5

    5. XM_047429844.1 → XP_047285800.1  ubiquitin-protein ligase E3B isoform X2

    6. XM_006719681.4 → XP_006719744.1  ubiquitin-protein ligase E3B isoform X3

      UniProtKB/TrEMBL
      B9EK57
      Conserved Domains (1) summary
      cd00078
      Location:682 → 1004
      HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...

    7. XM_006719682.3 → XP_006719745.1  ubiquitin-protein ligase E3B isoform X4

      UniProtKB/TrEMBL
      B9EK57
      Conserved Domains (1) summary
      cd00078
      Location:682 → 1004
      HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...

    8. XM_047429847.1 → XP_047285803.1  ubiquitin-protein ligase E3B isoform X3

    9. XM_005253987.3 → XP_005254044.1  ubiquitin-protein ligase E3B isoform X1

      See identical proteins and their annotated locations for XP_005254044.1

      UniProtKB/Swiss-Prot
      A5D8Z3, Q05BX9, Q659F7, Q7Z3V4, Q7Z7Q1, Q9BXZ4
      UniProtKB/TrEMBL
      B9EK57
      Conserved Domains (1) summary
      cd00078
      Location:682 → 1066
      HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...

    10. XM_047429845.1 → XP_047285801.1  ubiquitin-protein ligase E3B isoform X2

    11. XM_047429846.1 → XP_047285802.1  ubiquitin-protein ligase E3B isoform X3

    12. XM_047429849.1 → XP_047285805.1  ubiquitin-protein ligase E3B isoform X4

    13. XM_047429848.1 → XP_047285804.1  ubiquitin-protein ligase E3B isoform X3

    14. XM_047429850.1 → XP_047285806.1  ubiquitin-protein ligase E3B isoform X4

    15. XM_011538959.3 → XP_011537261.1  ubiquitin-protein ligase E3B isoform X1

      See identical proteins and their annotated locations for XP_011537261.1

      UniProtKB/Swiss-Prot
      A5D8Z3, Q05BX9, Q659F7, Q7Z3V4, Q7Z7Q1, Q9BXZ4
      UniProtKB/TrEMBL
      B9EK57
      Conserved Domains (1) summary
      cd00078
      Location:682 → 1066
      HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...

    16. XM_047429854.1 → XP_047285810.1  ubiquitin-protein ligase E3B isoform X7

    17. XM_017020196.2 → XP_016875685.1  ubiquitin-protein ligase E3B isoform X8

      UniProtKB/TrEMBL
      F5H6D6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      109452543..109519796
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373776.1 → XP_054229751.1  ubiquitin-protein ligase E3B isoform X5

    2. XM_054373778.1 → XP_054229753.1  ubiquitin-protein ligase E3B isoform X5

    3. XM_054373777.1 → XP_054229752.1  ubiquitin-protein ligase E3B isoform X5

    4. XM_054373779.1 → XP_054229754.1  ubiquitin-protein ligase E3B isoform X6

    5. XM_054373767.1 → XP_054229742.1  ubiquitin-protein ligase E3B isoform X2

    6. XM_054373769.1 → XP_054229744.1  ubiquitin-protein ligase E3B isoform X3

    7. XM_054373773.1 → XP_054229748.1  ubiquitin-protein ligase E3B isoform X4

    8. XM_054373771.1 → XP_054229746.1  ubiquitin-protein ligase E3B isoform X3

    9. XM_054373765.1 → XP_054229740.1  ubiquitin-protein ligase E3B isoform X1

    10. XM_054373768.1 → XP_054229743.1  ubiquitin-protein ligase E3B isoform X2

    11. XM_054373770.1 → XP_054229745.1  ubiquitin-protein ligase E3B isoform X3

    12. XM_054373774.1 → XP_054229749.1  ubiquitin-protein ligase E3B isoform X4

    13. XM_054373772.1 → XP_054229747.1  ubiquitin-protein ligase E3B isoform X3

    14. XM_054373775.1 → XP_054229750.1  ubiquitin-protein ligase E3B isoform X4

    15. XM_054373766.1 → XP_054229741.1  ubiquitin-protein ligase E3B isoform X1

    16. XM_054373780.1 → XP_054229755.1  ubiquitin-protein ligase E3B isoform X7

    17. XM_054373781.1 → XP_054229756.1  ubiquitin-protein ligase E3B isoform X8

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_183414.1: Suppressed sequence

      Description
      NM_183414.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z3V4.3 GenPept UniProtKB/Swiss-Prot:Q7Z3V4

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

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