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

    Gene ID: 55182, updated on 7-Jan-2024

    Summary

    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
    Predicted to enable ubiquitin protein ligase activity. Involved in positive regulation of canonical Wnt signaling pathway. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in brain (RPKM 10.7), testis (RPKM 7.1) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See RNF220 in Genome Data Viewer
    Location:
    1p34.1
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (44404783..44651724)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (44276080..44522650)
    105.20220307 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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
     
    Component Evidence Code Pubs
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    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 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    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)

    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_001319956.1NP_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:513553
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219442
      RNF220; E3 ubiquitin-protein ligase RNF220
    2. NM_001319957.2NP_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:300340
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:1229
      RNF220; E3 ubiquitin-protein ligase RNF220
    3. NM_001376486.1NP_001363415.1  E3 ubiquitin-protein ligase RNF220 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL122004, AL359373, AL596225
      Conserved Domains (2) summary
      cd16563
      Location:539579
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219468
      RNF220; E3 ubiquitin-protein ligase RNF220
    4. NM_001376487.1NP_001363416.1  E3 ubiquitin-protein ligase RNF220 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL122004, AL359373, AL596225
      Conserved Domains (2) summary
      cd16563
      Location:539579
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219468
      RNF220; E3 ubiquitin-protein ligase RNF220
    5. NM_001376488.1NP_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:513553
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219442
      RNF220; E3 ubiquitin-protein ligase RNF220
    6. NM_001376489.1NP_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:255295
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:18184
      RNF220; E3 ubiquitin-protein ligase RNF220
    7. NM_018150.4NP_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:513553
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219442
      RNF220; E3 ubiquitin-protein ligase RNF220

    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_000001.11 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

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

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

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

      Conserved Domains (1) summary
      pfam15926
      Location:217316
      RNF220; E3 ubiquitin-protein ligase RNF220
    4. XM_011541699.2XP_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:539579
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219468
      RNF220; E3 ubiquitin-protein ligase RNF220
    5. XM_047424280.1XP_047280236.1  E3 ubiquitin-protein ligase RNF220 isoform X1

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

      UniProtKB/Swiss-Prot
      B3KPJ3, B4DLZ9, E9PCS1, Q4KMX2, Q5VTB9, Q9NVP6
      Conserved Domains (2) summary
      cd16563
      Location:513553
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219442
      RNF220; E3 ubiquitin-protein ligase RNF220
    7. XM_011541698.3XP_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:539579
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219468
      RNF220; E3 ubiquitin-protein ligase RNF220
    8. XM_011541700.2XP_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:539579
      RING-HC_RNF220; RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins
      pfam15926
      Location:219468
      RNF220; E3 ubiquitin-protein ligase RNF220
    9. XM_047424281.1XP_047280237.1  E3 ubiquitin-protein ligase RNF220 isoform X3

    10. XM_047424282.1XP_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_054337414.1XP_054193389.1  E3 ubiquitin-protein ligase RNF220 isoform X4

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

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

      UniProtKB/Swiss-Prot
      B3KPJ3, B4DLZ9, E9PCS1, Q4KMX2, Q5VTB9, Q9NVP6
    4. XM_054337410.1XP_054193385.1  E3 ubiquitin-protein ligase RNF220 isoform X1

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

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

    7. XM_054337415.1XP_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 info@ncbi.nlm.nih.gov for further information.