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    RNF111 ring finger protein 111 [ Homo sapiens (human) ]

    Gene ID: 54778, updated on 5-May-2024

    Summary

    Official Symbol
    RNF111provided by HGNC
    Official Full Name
    ring finger protein 111provided by HGNC
    Primary source
    HGNC:HGNC:17384
    See related
    Ensembl:ENSG00000157450 MIM:605840; AllianceGenome:HGNC:17384
    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
    ARK; hRNF111
    Summary
    The protein encoded by this gene is a nuclear RING-domain containing E3 ubiquitin ligase. This protein interacts with the transforming growth factor (TGF) -beta/NODAL signaling pathway by promoting the ubiquitination and proteosomal degradation of negative regulators, like SMAD proteins, and thereby enhances TGF-beta target-gene transcription. As a modulator of the nodal signaling cascade, this gene plays a critical role in the induction of mesoderm during embryonic development. Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2012]
    Expression
    Ubiquitous expression in thyroid (RPKM 5.8), brain (RPKM 5.5) and 25 other tissues See more
    Orthologs
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    Genomic context

    See RNF111 in Genome Data Viewer
    Location:
    15q22.1-q22.2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (58987663..59097419)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (56789754..56899501)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (59279862..59389618)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9479 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:59219581-59220080 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6484 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9482 Neighboring gene SAFB like transcription modulator Neighboring gene ribosome binding factor A (putative) pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9484 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:59280581-59280745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:59283309-59283808 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6486 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:59317258-59317441 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:59317581-59318082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:59318083-59318582 Neighboring gene ribosomal protein L21 pseudogene 113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9485 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:59423635-59424134 Neighboring gene Sharpr-MPRA regulatory region 4265 Neighboring gene cyclin B2 Neighboring gene OCT4 hESC enhancer GRCh37_chr15:59453332-59453833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9486 Neighboring gene myosin IE Neighboring gene microRNA 2116

    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?

    Phenotypes

    EBI GWAS Catalog

    Description
    Common variation contributes to the genetic architecture of social communication traits.
    EBI GWAS Catalog
    Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
    EBI GWAS Catalog
    Variants in several genomic regions associated with asperger disorder.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ38008, DKFZp761D081, DKFZp313E0731, DKFZp686H1966

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SMAD binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables SUMO polymer binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables SUMO polymer binding IDA
    Inferred from Direct Assay
    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 ligase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables ubiquitin protein ligase activity TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    located_in PML body IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of protein-containing complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    E3 ubiquitin-protein ligase Arkadia
    Names
    Arkadia
    RING-type E3 ubiquitin transferase Arkadia
    NP_001257457.1
    NP_001257458.1
    NP_001257459.1
    NP_001317260.1
    NP_060080.6
    XP_006720638.1
    XP_016877825.1
    XP_047288657.1
    XP_047288658.1
    XP_047288659.1
    XP_047288660.1
    XP_047288661.1
    XP_047288662.1
    XP_047288663.1
    XP_047288664.1
    XP_047288665.1
    XP_047288666.1
    XP_047288667.1
    XP_047288668.1
    XP_047288669.1
    XP_047288670.1
    XP_047288671.1
    XP_047288672.1
    XP_047288673.1
    XP_047288674.1
    XP_047288675.1
    XP_047288676.1
    XP_047288677.1
    XP_047288678.1
    XP_047288679.1
    XP_054234216.1
    XP_054234217.1
    XP_054234218.1
    XP_054234219.1
    XP_054234220.1
    XP_054234221.1
    XP_054234222.1
    XP_054234223.1
    XP_054234224.1
    XP_054234225.1
    XP_054234226.1
    XP_054234227.1
    XP_054234228.1
    XP_054234229.1
    XP_054234230.1
    XP_054234231.1
    XP_054234232.1
    XP_054234233.1
    XP_054234234.1
    XP_054234235.1
    XP_054234236.1
    XP_054234237.1
    XP_054234238.1
    XP_054234239.1
    XP_054234240.1

    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_001270528.2NP_001257457.1  E3 ubiquitin-protein ligase Arkadia isoform 1

      See identical proteins and their annotated locations for NP_001257457.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AC025918, AI189975, AL157474, AL832089, BM986870, BX538130, BX647259, CN420669, N24855
      Consensus CDS
      CCDS58365.1
      Related
      ENSP00000453872.1, ENST00000559209.5
      Conserved Domains (3) summary
      pfam05647
      Location:407474
      Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
      pfam13639
      Location:943984
      zf-RING_2; Ring finger domain
      pfam15303
      Location:18251
      RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
    2. NM_001270529.2NP_001257458.1  E3 ubiquitin-protein ligase Arkadia isoform 3

      See identical proteins and their annotated locations for NP_001257458.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame segment in the 3' coding region, compared to variant 1, which results in a shorter protein (isoform 3), compared to isoform 1.
      Source sequence(s)
      AC025918, AI189975, AL157474, BC060862, BM986870, BX538130, BX647259, CN420669, N24855
      Conserved Domains (3) summary
      pfam05647
      Location:407474
      Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
      pfam13639
      Location:933974
      zf-RING_2; Ring finger domain
      pfam15303
      Location:18251
      RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
    3. NM_001270530.2NP_001257459.1  E3 ubiquitin-protein ligase Arkadia isoform 4

      See identical proteins and their annotated locations for NP_001257459.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has multiple differences in the 3' coding region, compared to variant 1, which results in a shorter protein (isoform 4), compared to isoform 1.
      Source sequence(s)
      AC025918, AI189975, AL832089, BC020984, BM986870, BX538130, BX647259, CN420669, DA720863, N24855
      Consensus CDS
      CCDS58366.1
      UniProtKB/Swiss-Prot
      C9JUS4, H0YN55, Q6P9A4, Q6ZMU2, Q6ZNA4, Q7L428, Q7Z346, Q8N1P9, Q8WUA3, Q9NSR1
      Related
      ENSP00000452732.1, ENST00000557998.5
      Conserved Domains (3) summary
      pfam05647
      Location:407474
      Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
      pfam13639
      Location:942983
      zf-RING_2; Ring finger domain
      pfam15303
      Location:18251
      RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
    4. NM_001330331.2NP_001317260.1  E3 ubiquitin-protein ligase Arkadia isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (5) is longer than isoform 1.
      Source sequence(s)
      AC025918, AC092757, AI189975
      Consensus CDS
      CCDS81888.1
      Related
      ENSP00000453015.1, ENST00000561186.5
      Conserved Domains (3) summary
      pfam05647
      Location:407474
      Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
      pfam13639
      Location:951992
      zf-RING_2; Ring finger domain
      pfam15303
      Location:18251
      RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
    5. NM_017610.8NP_060080.6  E3 ubiquitin-protein ligase Arkadia isoform 2

      See identical proteins and their annotated locations for NP_060080.6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment in the 3' coding region, compared to variant 1, which results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC025918, AI189975, AL157474, AL832089, BM986870, BX538130, BX647259, CN420669, N24855
      Consensus CDS
      CCDS10169.1
      Related
      ENSP00000288199.5, ENST00000348370.9
      Conserved Domains (3) summary
      pfam05647
      Location:407474
      Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
      pfam13639
      Location:934975
      zf-RING_2; Ring finger domain
      pfam15303
      Location:18251
      RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      58987663..59097419
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047432702.1XP_047288658.1  E3 ubiquitin-protein ligase Arkadia isoform X1

    2. XM_047432708.1XP_047288664.1  E3 ubiquitin-protein ligase Arkadia isoform X4

    3. XM_047432713.1XP_047288669.1  E3 ubiquitin-protein ligase Arkadia isoform X9

    4. XM_047432717.1XP_047288673.1  E3 ubiquitin-protein ligase Arkadia isoform X12

    5. XM_047432721.1XP_047288677.1  E3 ubiquitin-protein ligase Arkadia isoform X15

    6. XM_047432720.1XP_047288676.1  E3 ubiquitin-protein ligase Arkadia isoform X14

    7. XM_047432723.1XP_047288679.1  E3 ubiquitin-protein ligase Arkadia isoform X16

    8. XM_047432701.1XP_047288657.1  E3 ubiquitin-protein ligase Arkadia isoform X1

    9. XM_047432706.1XP_047288662.1  E3 ubiquitin-protein ligase Arkadia isoform X3

    10. XM_047432707.1XP_047288663.1  E3 ubiquitin-protein ligase Arkadia isoform X4

    11. XM_047432711.1XP_047288667.1  E3 ubiquitin-protein ligase Arkadia isoform X7

    12. XM_047432705.1XP_047288661.1  E3 ubiquitin-protein ligase Arkadia isoform X2

    13. XM_047432709.1XP_047288665.1  E3 ubiquitin-protein ligase Arkadia isoform X5

    14. XM_047432710.1XP_047288666.1  E3 ubiquitin-protein ligase Arkadia isoform X6

    15. XM_047432712.1XP_047288668.1  E3 ubiquitin-protein ligase Arkadia isoform X8

    16. XM_006720575.4XP_006720638.1  E3 ubiquitin-protein ligase Arkadia isoform X9

      Conserved Domains (3) summary
      pfam05647
      Location:430494
      Epiglycanin_TR; Tandem-repeating region of mucin, epiglycanin-like
      pfam13639
      Location:9741015
      zf-RING_2; Ring finger domain
      pfam15303
      Location:41274
      RNF111_N; E3 ubiquitin-protein ligase Arkadia N-terminus
    17. XM_047432715.1XP_047288671.1  E3 ubiquitin-protein ligase Arkadia isoform X11

    18. XM_047432716.1XP_047288672.1  E3 ubiquitin-protein ligase Arkadia isoform X12

    19. XM_017022336.2XP_016877825.1  E3 ubiquitin-protein ligase Arkadia isoform X15

      Conserved Domains (2) summary
      pfam06933
      Location:429490
      SSP160; Special lobe-specific silk protein SSP160
      cd16474
      Location:9561000
      RING-H2_RNF111_like; RING finger, H2 subclass, found in RING finger proteins RNF111, RNF165, and similar proteins
    20. XM_047432714.1XP_047288670.1  E3 ubiquitin-protein ligase Arkadia isoform X10

    21. XM_047432718.1XP_047288674.1  E3 ubiquitin-protein ligase Arkadia isoform X13

    22. XM_047432719.1XP_047288675.1  E3 ubiquitin-protein ligase Arkadia isoform X14

    23. XM_047432722.1XP_047288678.1  E3 ubiquitin-protein ligase Arkadia isoform X16

    24. XM_047432703.1XP_047288659.1  E3 ubiquitin-protein ligase Arkadia isoform X1

    25. XM_047432704.1XP_047288660.1  E3 ubiquitin-protein ligase Arkadia isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      56789754..56899501
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378242.1XP_054234217.1  E3 ubiquitin-protein ligase Arkadia isoform X1

    2. XM_054378248.1XP_054234223.1  E3 ubiquitin-protein ligase Arkadia isoform X4

    3. XM_054378254.1XP_054234229.1  E3 ubiquitin-protein ligase Arkadia isoform X9

    4. XM_054378258.1XP_054234233.1  E3 ubiquitin-protein ligase Arkadia isoform X12

    5. XM_054378263.1XP_054234238.1  E3 ubiquitin-protein ligase Arkadia isoform X15

    6. XM_054378261.1XP_054234236.1  E3 ubiquitin-protein ligase Arkadia isoform X14

    7. XM_054378265.1XP_054234240.1  E3 ubiquitin-protein ligase Arkadia isoform X16

    8. XM_054378241.1XP_054234216.1  E3 ubiquitin-protein ligase Arkadia isoform X1

    9. XM_054378246.1XP_054234221.1  E3 ubiquitin-protein ligase Arkadia isoform X3

    10. XM_054378247.1XP_054234222.1  E3 ubiquitin-protein ligase Arkadia isoform X4

    11. XM_054378251.1XP_054234226.1  E3 ubiquitin-protein ligase Arkadia isoform X7

    12. XM_054378245.1XP_054234220.1  E3 ubiquitin-protein ligase Arkadia isoform X2

    13. XM_054378249.1XP_054234224.1  E3 ubiquitin-protein ligase Arkadia isoform X5

    14. XM_054378250.1XP_054234225.1  E3 ubiquitin-protein ligase Arkadia isoform X6

    15. XM_054378252.1XP_054234227.1  E3 ubiquitin-protein ligase Arkadia isoform X8

    16. XM_054378253.1XP_054234228.1  E3 ubiquitin-protein ligase Arkadia isoform X9

    17. XM_054378256.1XP_054234231.1  E3 ubiquitin-protein ligase Arkadia isoform X11

    18. XM_054378257.1XP_054234232.1  E3 ubiquitin-protein ligase Arkadia isoform X12

    19. XM_054378262.1XP_054234237.1  E3 ubiquitin-protein ligase Arkadia isoform X15

    20. XM_054378255.1XP_054234230.1  E3 ubiquitin-protein ligase Arkadia isoform X10

    21. XM_054378259.1XP_054234234.1  E3 ubiquitin-protein ligase Arkadia isoform X13

    22. XM_054378260.1XP_054234235.1  E3 ubiquitin-protein ligase Arkadia isoform X14

    23. XM_054378264.1XP_054234239.1  E3 ubiquitin-protein ligase Arkadia isoform X16

    24. XM_054378243.1XP_054234218.1  E3 ubiquitin-protein ligase Arkadia isoform X1

    25. XM_054378244.1XP_054234219.1  E3 ubiquitin-protein ligase Arkadia isoform X1