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

Gene ID: 54778, updated on 5-Mar-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

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