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    RNF220 ring finger protein 220 [ Homo sapiens (human) ]

    Gene ID: 55182, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RNF220provided by HGNC
    Official Full Name
    ring finger protein 220provided by HGNC
    Primary source
    HGNC:HGNC:25552
    See related
    Ensembl:ENSG00000187147 MIM:616136; AllianceGenome:HGNC:25552
    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
    Also known as
    HLD23; C1orf164
    Summary
    Enables beta-catenin binding activity. Involved in positive regulation of canonical Wnt signaling pathway. Acts upstream of or within positive regulation of DNA-binding transcription factor activity and protein monoubiquitination. Located in nuclear lamina. Part of protein-containing complex. Implicated in hypomyelinating leukodystrophy 23. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in brain (RPKM 10.7), testis (RPKM 7.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RNF220 in Genome Data Viewer
    Location:
    1p34.1
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (44404783..44651724)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (44276080..44522650)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (44870832..45117396)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ERI1 exoribonuclease family member 3 Neighboring gene small nucleolar RNA, H/ACA box 110 Neighboring gene Sharpr-MPRA regulatory region 3045 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_8150 Neighboring gene NANOG hESC enhancer GRCh37_chr1:44805333-44805834 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:44820763-44821263 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:44834096-44834628 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_8167 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:44839934-44840144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44871820-44872342 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:44874109-44874785 Neighboring gene RNA, U6 small nuclear 369, pseudogene Neighboring gene MPRA-validated peak196 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr1:44902025-44902526 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44949184-44950063 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44950064-44950942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44961950-44962450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44972171-44972671 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44972832-44973468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44973469-44974104 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:44987221-44987386 Neighboring gene VISTA enhancer hs280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44988460-44989317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45007461-45008268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45011382-45011908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 810 Neighboring gene microRNA 5584 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:45060915-45061086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:45075197-45075758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:45075759-45076318 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 939 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45097341-45097888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 941 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:45098438-45098985 Neighboring gene uncharacterized LOC107984950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:45115956-45116537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 942 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:45139597-45140098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 814 Neighboring gene uncharacterized LOC105378690 Neighboring gene transmembrane protein 53 Neighboring gene small nucleolar RNA, C/D box 145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 815 Neighboring gene armadillo like helical domain containing 1 Neighboring gene RNA, U5F small nuclear 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. A homozygous RNF220 mutation leads to male infertility with small-headed sperm. Jiang X, et al. Gene, 2019 Mar 10. PMID 30500349
    2. CircRNF220, not its linear cognate gene RNF220, regulates cell growth and is associated with relapse in pediatric acute myeloid leukemia. Liu X, et al. Mol Cancer, 2021 Oct 26. PMID 34702297, Free PMC Article
    3. Smurf1 and Smurf2 mediated polyubiquitination and degradation of RNF220 suppresses Shh-group medulloblastoma. Li Y, et al. Cell Death Dis, 2023 Aug 3. PMID 37537194, Free PMC Article
    4. RNF220 promotes the proliferation of leukaemic cells and reduces the degradation of the Cyclin D1 protein through USP22. Pan Y, et al. Blood Cells Mol Dis, 2021 Feb. PMID 32896826
    5. Ring finger 220 promotes the stemness and progression of colon cancer cells via Ubiquitin specific peptidase 22-BMI1 axis. Yan J, et al. Bioengineered, 2021 Dec. PMID 34753387, Free PMC Article

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Smurf1 and Smurf2 mediated polyubiquitination and degradation of RNF220 suppresses Shh-group medulloblastoma.
      Title: Smurf1 and Smurf2 mediated polyubiquitination and degradation of RNF220 suppresses Shh-group medulloblastoma.
    2. Sequential stabilization of RNF220 by RLIM and ZC4H2 during cerebellum development and Shh-group medulloblastoma progression.
      Title: Sequential stabilization of RNF220 by RLIM and ZC4H2 during cerebellum development and Shh-group medulloblastoma progression.
    3. CircRNF220, not its linear cognate gene RNF220, regulates cell growth and is associated with relapse in pediatric acute myeloid leukemia.
      Title: CircRNF220, not its linear cognate gene RNF220, regulates cell growth and is associated with relapse in pediatric acute myeloid leukemia.
    4. Ring finger 220 promotes the stemness and progression of colon cancer cells via Ubiquitin specific peptidase 22-BMI1 axis.
      Title: Ring finger 220 promotes the stemness and progression of colon cancer cells via Ubiquitin specific peptidase 22-BMI1 axis.
    5. Biallelic mutations in RNF220 cause laminopathies featuring leukodystrophy, ataxia and deafness.
      Title: Biallelic mutations in RNF220 cause laminopathies featuring leukodystrophy, ataxia and deafness.
    6. RNF220 promotes the proliferation of leukaemic cells and reduces the degradation of the Cyclin D1 protein through USP22.
      Title: RNF220 promotes the proliferation of leukaemic cells and reduces the degradation of the Cyclin D1 protein through USP22.
    7. This variant could promote the RNF220 protein degradation.
      Title: A homozygous RNF220 mutation leads to male infertility with small-headed sperm.
    8. RNF220 interacts with USP7, a ubiquitin-specific peptidase, which is required for RNF220 to stabilize beta-catenin.
      Title: The ubiquitin ligase RNF220 enhances canonical Wnt signaling through USP7-mediated deubiquitination of β-catenin.
    9. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10597

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables beta-catenin binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin-protein transferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in dorsal/ventral neural tube patterning IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in noradrenergic neuron development IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within positive regulation of DNA-binding transcription factor activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein autoubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within protein monoubiquitination IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of postsynaptic neurotransmitter receptor internalization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of transcription regulatory region DNA binding IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear lamina IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in postsynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase RNF220
    Names
    RING-type E3 ubiquitin transferase RNF220
    NP_001306885.1
    NP_001306886.1
    NP_001363415.1
    NP_001363416.1
    NP_001363417.1
    NP_001363418.1
    NP_060620.2
    XP_006710798.1
    XP_011540000.1
    XP_011540001.1
    XP_011540002.1
    XP_016857114.1
    XP_047280225.1
    XP_047280233.1
    XP_047280236.1
    XP_047280237.1
    XP_047280238.1
    XP_054193384.1
    XP_054193385.1
    XP_054193386.1
    XP_054193387.1
    XP_054193388.1
    XP_054193389.1
    XP_054193390.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001319956.1 → NP_001306885.1  E3 ubiquitin-protein ligase RNF220 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      BC034221, BC098266, CN285725
      Consensus CDS
      CCDS510.1
      UniProtKB/Swiss-Prot
      B3KPJ3, B4DLZ9, E9PCS1, Q4KMX2, Q5VTB9, Q9NVP6
      Related
      ENSP00000347548.2, ENST00000355387.6
      Conserved Domains (2) summary
      cd16563
      Location:513 → 553
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219 → 442
      RNF220; E3 ubiquitin-protein ligase RNF220

    2. NM_001319957.2 → NP_001306886.1  E3 ubiquitin-protein ligase RNF220 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' terminal exon, differs in the 5' UTR, lacks a portion of the coding region, uses a downstrean in-frame start codon and uses an alternate in-frame splice site in the coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AK025744, AK297228, BC034221, DC340836
      UniProtKB/Swiss-Prot
      Q5VTB9
      Conserved Domains (2) summary
      cd16563
      Location:300 → 340
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:1 → 229
      RNF220; E3 ubiquitin-protein ligase RNF220

    3. NM_001376486.1 → NP_001363415.1  E3 ubiquitin-protein ligase RNF220 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL122004, AL359373, AL596225
      Conserved Domains (2) summary
      cd16563
      Location:539 → 579
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219 → 468
      RNF220; E3 ubiquitin-protein ligase RNF220

    4. NM_001376487.1 → NP_001363416.1  E3 ubiquitin-protein ligase RNF220 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL122004, AL359373, AL596225
      Conserved Domains (2) summary
      cd16563
      Location:539 → 579
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219 → 468
      RNF220; E3 ubiquitin-protein ligase RNF220

    5. NM_001376488.1 → NP_001363417.1  E3 ubiquitin-protein ligase RNF220 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL122004, AL359373, AL596225
      Consensus CDS
      CCDS510.1
      UniProtKB/Swiss-Prot
      B3KPJ3, B4DLZ9, E9PCS1, Q4KMX2, Q5VTB9, Q9NVP6
      Conserved Domains (2) summary
      cd16563
      Location:513 → 553
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219 → 442
      RNF220; E3 ubiquitin-protein ligase RNF220

    6. NM_001376489.1 → NP_001363418.1  E3 ubiquitin-protein ligase RNF220 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL122004, AL596225
      UniProtKB/TrEMBL
      B4DJE2
      Related
      ENSP00000335580.7, ENST00000335497.11
      Conserved Domains (2) summary
      cd16563
      Location:255 → 295
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:18 → 184
      RNF220; E3 ubiquitin-protein ligase RNF220

    7. NM_018150.4 → NP_060620.2  E3 ubiquitin-protein ligase RNF220 isoform 1

      See identical proteins and their annotated locations for NP_060620.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AK025744, BC034221, CN285725
      Consensus CDS
      CCDS510.1
      UniProtKB/Swiss-Prot
      B3KPJ3, B4DLZ9, E9PCS1, Q4KMX2, Q5VTB9, Q9NVP6
      Related
      ENSP00000354872.2, ENST00000361799.7
      Conserved Domains (2) summary
      cd16563
      Location:513 → 553
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219 → 442
      RNF220; E3 ubiquitin-protein ligase RNF220

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      44404783..44651724
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047424277.1 → XP_047280233.1  E3 ubiquitin-protein ligase RNF220 isoform X1

    2. XM_047424269.1 → XP_047280225.1  E3 ubiquitin-protein ligase RNF220 isoform X1

    3. XM_006710735.5 → XP_006710798.1  E3 ubiquitin-protein ligase RNF220 isoform X4

      Conserved Domains (1) summary
      pfam15926
      Location:217 → 316
      RNF220; E3 ubiquitin-protein ligase RNF220

    4. XM_011541699.2 → XP_011540001.1  E3 ubiquitin-protein ligase RNF220 isoform X1

      See identical proteins and their annotated locations for XP_011540001.1

      Conserved Domains (2) summary
      cd16563
      Location:539 → 579
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219 → 468
      RNF220; E3 ubiquitin-protein ligase RNF220

    5. XM_047424280.1 → XP_047280236.1  E3 ubiquitin-protein ligase RNF220 isoform X1

    6. XM_017001625.3 → XP_016857114.1  E3 ubiquitin-protein ligase RNF220 isoform X2

      UniProtKB/Swiss-Prot
      B3KPJ3, B4DLZ9, E9PCS1, Q4KMX2, Q5VTB9, Q9NVP6
      Conserved Domains (2) summary
      cd16563
      Location:513 → 553
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219 → 442
      RNF220; E3 ubiquitin-protein ligase RNF220

    7. XM_011541698.3 → XP_011540000.1  E3 ubiquitin-protein ligase RNF220 isoform X1

      See identical proteins and their annotated locations for XP_011540000.1

      Conserved Domains (2) summary
      cd16563
      Location:539 → 579
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219 → 468
      RNF220; E3 ubiquitin-protein ligase RNF220

    8. XM_011541700.2 → XP_011540002.1  E3 ubiquitin-protein ligase RNF220 isoform X1

      See identical proteins and their annotated locations for XP_011540002.1

      Conserved Domains (2) summary
      cd16563
      Location:539 → 579
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219 → 468
      RNF220; E3 ubiquitin-protein ligase RNF220

    9. XM_047424281.1 → XP_047280237.1  E3 ubiquitin-protein ligase RNF220 isoform X3

    10. XM_047424282.1 → XP_047280238.1  E3 ubiquitin-protein ligase RNF220 isoform X5

      UniProtKB/TrEMBL
      Q5TDE7
      Related
      ENSP00000388533.2, ENST00000440132.2

    RNA

    1. XR_007061417.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      44276080..44522650
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337414.1 → XP_054193389.1  E3 ubiquitin-protein ligase RNF220 isoform X4

    2. XM_054337409.1 → XP_054193384.1  E3 ubiquitin-protein ligase RNF220 isoform X1

    3. XM_054337412.1 → XP_054193387.1  E3 ubiquitin-protein ligase RNF220 isoform X2

      UniProtKB/Swiss-Prot
      B3KPJ3, B4DLZ9, E9PCS1, Q4KMX2, Q5VTB9, Q9NVP6

    4. XM_054337410.1 → XP_054193385.1  E3 ubiquitin-protein ligase RNF220 isoform X1

    5. XM_054337411.1 → XP_054193386.1  E3 ubiquitin-protein ligase RNF220 isoform X1

    6. XM_054337413.1 → XP_054193388.1  E3 ubiquitin-protein ligase RNF220 isoform X3

    7. XM_054337415.1 → XP_054193390.1  E3 ubiquitin-protein ligase RNF220 isoform X5

      UniProtKB/TrEMBL
      Q5TDE7

    RNA

    1. XR_008486089.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_016501.2: Suppressed sequence

      Description
      NM_016501.2: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VTB9.1 GenPept UniProtKB/Swiss-Prot:Q5VTB9

    Gene LinkOut

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

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