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    LRSAM1 leucine rich repeat and sterile alpha motif containing 1 [ Homo sapiens (human) ]

    Gene ID: 90678, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LRSAM1provided by HGNC
    Official Full Name
    leucine rich repeat and sterile alpha motif containing 1provided by HGNC
    Primary source
    HGNC:HGNC:25135
    See related
    Ensembl:ENSG00000148356 MIM:610933; AllianceGenome:HGNC:25135
    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
    TAL; CMT2P; RIFLE
    Summary
    This gene encodes a ring finger protein involved in a variety of functions, including regulation of signaling pathways and cell adhesion, mediation of self-ubiquitylation, and involvement in cargo sorting during receptor endocytosis. Mutations in this gene have been associated with Charcot-Marie-Tooth disease. Multiple transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jan 2012]
    Expression
    Ubiquitous expression in skin (RPKM 9.6), bone marrow (RPKM 7.7) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRSAM1 in Genome Data Viewer
    Location:
    9q33.3-q34.11
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (127451486..127503501)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (139658436..139710463)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130213765..130265780)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:130185748-130186690 Neighboring gene zinc finger protein 79 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29040 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:130211857-130212400 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130212943-130213486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29042 Neighboring gene small nucleolar RNA, H/ACA box 65 Neighboring gene ribosomal protein L12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130226032-130226532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130226533-130227033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130251390-130251970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130251971-130252551 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130256483-130257002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130262849-130263350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130266531-130267404 Neighboring gene niban apoptosis regulator 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130285667-130286168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130286169-130286668 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130287309-130287861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130293634-130294194 Neighboring gene uncharacterized LOC105376281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130314335-130314834 Neighboring gene Sharpr-MPRA regulatory region 14561 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130323322-130324026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130324732-130325436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130325437-130326140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130328804-130329344 Neighboring gene FAM129B intron CAGE-defined low expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130331508-130332048 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130332049-130332588 Neighboring gene Sharpr-MPRA regulatory region 10550 Neighboring gene uncharacterized LOC124902276

    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. A novel mutation in LRSAM1 causes axonal Charcot-Marie-Tooth disease with dominant inheritance. Engeholm M, et al. BMC Neurol, 2014 Jun 3. PMID 24894446, Free PMC Article
    2. A novel mutation of LRSAM1 in a Chinese family with Charcot-Marie-Tooth disease. Zhao G, et al. J Peripher Nerv Syst, 2018 Mar. PMID 29341362
    3. A novel LRSAM1 mutation is associated with autosomal dominant axonal Charcot-Marie-Tooth disease. Nicolaou P, et al. Eur J Hum Genet, 2013 Feb. PMID 22781092, Free PMC Article
    4. LRSAM1 E3 ubiquitin ligase: molecular neurobiological perspectives linked with brain diseases. Mishra R, et al. Cell Mol Life Sci, 2019 Jun. PMID 30826859, Free PMC Article
    5. LRSAM1 variants and founder effect in French families with ataxic form of Charcot-Marie-Tooth type 2. Peretti A, et al. Eur J Hum Genet, 2019 Sep. PMID 30996334, Free PMC Article

    See all (73) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A novel mutation in the LRSAM1 gene in a family with early onset autosomal dominant Charcot-Marie-Tooth type 2P.
      Title: A novel mutation in the LRSAM1 gene in a family with early onset autosomal dominant Charcot-Marie-Tooth type 2P.
    2. [Novel MFN2, BSCL2 and LRSAM1 variants in a cohort of Chinese patients with Charcot-Marie-Tooth disease].
      Title: [Novel MFN2, BSCL2 and LRSAM1 variants in a cohort of Chinese patients with Charcot-Marie-Tooth disease].
    3. C698R mutation in Lrsam1 gene impairs nerve regeneration in a CMT2P mouse model.
      Title: C698R mutation in Lrsam1 gene impairs nerve regeneration in a CMT2P mouse model.
    4. LRSAM1 E3 ubiquitin ligase promotes proteasomal clearance of E6-AP protein.
      Title: LRSAM1 E3 ubiquitin ligase promotes proteasomal clearance of E6-AP protein.
    5. Location matters - Genotype-phenotype correlation in LRSAM1 mutations associated with rare Charcot-Marie-Tooth neuropathy CMT2P.
      Title: Location matters - Genotype-phenotype correlation in LRSAM1 mutations associated with rare Charcot-Marie-Tooth neuropathy CMT2P.
    6. Ubiquitin ligase LRSAM1 suppresses neurodegenerative diseases linked aberrant proteins induced cell death.
      Title: Ubiquitin ligase LRSAM1 suppresses neurodegenerative diseases linked aberrant proteins induced cell death.
    7. Identification of novel pathogenic copy number variations in Charcot-Marie-Tooth disease.
      Title: Identification of novel pathogenic copy number variations in Charcot-Marie-Tooth disease.
    8. Our results confirm the localization of variants in its catalytic C-terminal RING domain and broaden the phenotypic spectrum of LRSAM1-related neuropathies, including painful and predominantly sensory ataxic forms.
      Title: LRSAM1 variants and founder effect in French families with ataxic form of Charcot-Marie-Tooth type 2.
    9. We report a novel LRSAM1 mutation c.2021-2024del (p.E674VfsX11) in 4 members of a Chinese autosomal dominant Charcot-Marie-Tooth disease type 2 family
      Title: A novel mutation of LRSAM1 in a Chinese family with Charcot-Marie-Tooth disease.
    10. The article systematically represents the molecular functions, nature and detailed characterization of LRSAM1 E3 ubiquitin ligase, which are linked to molecular mechanisms of neurodegeneration. (Review)
      Title: LRSAM1 E3 ubiquitin ligase: molecular neurobiological perspectives linked with brain diseases.
    Submit: New GeneRIF Correction See all GeneRIFs (25)

    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
    Charcot-Marie-Tooth disease axonal type 2P
    MedGen: C3280797 OMIM: 614436 GeneReviews: Not available
    		Compare labs

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag TAL, a Tsg101-associated ligase, binds and ubiquitinates Tsg101; TAL-mediated binding and ubiquitination of Tsg101 cooperatively regulate release of HIV-1 Gag PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ31641

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin protein ligase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of xenophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein autoubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein polyubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ubiquitin-dependent endocytosis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in viral budding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase LRSAM1
    Names
    RING finger leucine repeat rich
    RING-type E3 ubiquitin transferase LRSAM1
    Tsg101-associated ligase
    NP_001005373.1
    NP_001005374.1
    NP_001177652.1
    NP_001371071.1
    NP_001371072.1
    NP_001371073.1
    NP_612370.3
    XP_047280014.1
    XP_047280015.1
    XP_054220121.1
    XP_054220122.1

    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_032008.1 RefSeqGene

      Range
      5001..57016
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_373

    mRNA and Protein(s)

    1. NM_001005373.4 → NP_001005373.1  E3 ubiquitin-protein ligase LRSAM1 isoform 1

      See identical proteins and their annotated locations for NP_001005373.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).
      Source sequence(s)
      AL445222
      Consensus CDS
      CCDS6873.1
      UniProtKB/Swiss-Prot
      Q5VVV0, Q6UWE0, Q8NB40, Q96GT5, Q96MX5, Q96MZ7
      UniProtKB/TrEMBL
      A0A6Q8PGF7
      Related
      ENSP00000300417.6, ENST00000300417.11
      Conserved Domains (5) summary
      cd09523
      Location:567 → 631
      SAM_TAL; SAM domain of TAL subfamily
      COG4886
      Location:65 → 181
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:33 → 54
      LRR_RI; leucine-rich repeat [structural motif]
      cd16515
      Location:674 → 713
      RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins
      pfam17380
      Location:257 → 474
      DUF5401; Family of unknown function (DUF5401)

    2. NM_001005374.4 → NP_001005374.1  E3 ubiquitin-protein ligase LRSAM1 isoform 1

      See identical proteins and their annotated locations for NP_001005374.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).
      Source sequence(s)
      AY358830, BC009239
      Consensus CDS
      CCDS6873.1
      UniProtKB/Swiss-Prot
      Q5VVV0, Q6UWE0, Q8NB40, Q96GT5, Q96MX5, Q96MZ7
      UniProtKB/TrEMBL
      A0A6Q8PGF7
      Related
      ENSP00000362419.1, ENST00000373322.1
      Conserved Domains (5) summary
      cd09523
      Location:567 → 631
      SAM_TAL; SAM domain of TAL subfamily
      COG4886
      Location:65 → 181
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:33 → 54
      LRR_RI; leucine-rich repeat [structural motif]
      cd16515
      Location:674 → 713
      RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins
      pfam17380
      Location:257 → 474
      DUF5401; Family of unknown function (DUF5401)

    3. NM_001190723.3 → NP_001177652.1  E3 ubiquitin-protein ligase LRSAM1 isoform 2

      See identical proteins and their annotated locations for NP_001177652.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AK056203, BC009239, DA165729
      Consensus CDS
      CCDS55347.1
      UniProtKB/TrEMBL
      A0A6Q8PFT9
      Related
      ENSP00000362421.4, ENST00000373324.8
      Conserved Domains (8) summary
      cd09523
      Location:540 → 604
      SAM_TAL; SAM domain of TAL subfamily
      smart00454
      Location:544 → 604
      SAM; Sterile alpha motif
      cd00116
      Location:67 → 162
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00033
      Location:33 → 54
      LRR_RI; leucine-rich repeat [structural motif]
      pfam10267
      Location:308 → 416
      Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein
      pfam12799
      Location:127 → 166
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:127 → 181
      LRR_8; Leucine rich repeat
      pfam13920
      Location:647 → 689
      zf-C3HC4_3; Zinc finger, C3HC4 type (RING finger)

    4. NM_001384142.1 → NP_001371071.1  E3 ubiquitin-protein ligase LRSAM1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL445222
      Consensus CDS
      CCDS6873.1
      UniProtKB/Swiss-Prot
      Q5VVV0, Q6UWE0, Q8NB40, Q96GT5, Q96MX5, Q96MZ7
      UniProtKB/TrEMBL
      A0A6Q8PGF7
      Conserved Domains (5) summary
      cd09523
      Location:567 → 631
      SAM_TAL; SAM domain of TAL subfamily
      COG4886
      Location:65 → 181
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:33 → 54
      LRR_RI; leucine-rich repeat [structural motif]
      cd16515
      Location:674 → 713
      RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins
      pfam17380
      Location:257 → 474
      DUF5401; Family of unknown function (DUF5401)

    5. NM_001384143.1 → NP_001371072.1  E3 ubiquitin-protein ligase LRSAM1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL445222
      Consensus CDS
      CCDS94485.1
      UniProtKB/TrEMBL
      A0A6Q8PFT9, A0A6Q8PGW1
      Related
      ENSP00000501598.1, ENST00000675572.1
      Conserved Domains (5) summary
      cd09523
      Location:536 → 598
      SAM_TAL; SAM domain of TAL subfamily
      COG4886
      Location:65 → 181
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:33 → 54
      LRR_RI; leucine-rich repeat [structural motif]
      cd16515
      Location:641 → 680
      RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins
      pfam17380
      Location:257 → 474
      DUF5401; Family of unknown function (DUF5401)

    6. NM_001384144.1 → NP_001371073.1  E3 ubiquitin-protein ligase LRSAM1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL445222
      Conserved Domains (4) summary
      PRK12704
      Location:27 → 113
      PRK12704; phosphodiesterase; Provisional
      cd16515
      Location:411 → 450
      RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins
      pfam17380
      Location:3 → 211
      DUF5401; Family of unknown function (DUF5401)
      cl15755
      Location:304 → 368
      SAM_superfamily; SAM (Sterile alpha motif )

    7. NM_138361.5 → NP_612370.3  E3 ubiquitin-protein ligase LRSAM1 isoform 1

      See identical proteins and their annotated locations for NP_612370.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1, 2 and 3 encode the same isoform (1).
      Source sequence(s)
      AI364608, AK091589, BC009239, DA726792
      Consensus CDS
      CCDS6873.1
      UniProtKB/Swiss-Prot
      Q5VVV0, Q6UWE0, Q8NB40, Q96GT5, Q96MX5, Q96MZ7
      UniProtKB/TrEMBL
      A0A6Q8PGF7
      Related
      ENSP00000322937.4, ENST00000323301.8
      Conserved Domains (5) summary
      cd09523
      Location:567 → 631
      SAM_TAL; SAM domain of TAL subfamily
      COG4886
      Location:65 → 181
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:33 → 54
      LRR_RI; leucine-rich repeat [structural motif]
      cd16515
      Location:674 → 713
      RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins
      pfam17380
      Location:257 → 474
      DUF5401; Family of unknown function (DUF5401)

    RNA

    1. NR_168891.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL445222
      Related
      ENST00000498513.6

    2. NR_168892.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL445222
      Related
      ENST00000675641.1

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      127451486..127503501
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047424058.1 → XP_047280014.1  E3 ubiquitin-protein ligase LRSAM1 isoform X1

      UniProtKB/TrEMBL
      A0A6Q8PGW1

    2. XM_047424059.1 → XP_047280015.1  E3 ubiquitin-protein ligase LRSAM1 isoform X2

      Related
      ENST00000676399.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      139658436..139710463
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054364146.1 → XP_054220121.1  E3 ubiquitin-protein ligase LRSAM1 isoform X1

    2. XM_054364147.1 → XP_054220122.1  E3 ubiquitin-protein ligase LRSAM1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6UWE0.1 GenPept UniProtKB/Swiss-Prot:Q6UWE0

    Gene LinkOut

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

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