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RBCK1 RANBP2-type and C3HC4-type zinc finger containing 1 [ Homo sapiens (human) ]

Gene ID: 10616, updated on 19-Aug-2018

Summary

Official Symbol
RBCK1provided by HGNC
Official Full Name
RANBP2-type and C3HC4-type zinc finger containing 1provided by HGNC
Primary source
HGNC:HGNC:15864
See related
Ensembl:ENSG00000125826 MIM:610924; Vega:OTTHUMG00000031634
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
XAP3; XAP4; HOIL1; PBMEI; PGBM1; RBCK2; RNF54; HOIL-1; ZRANB4; C20orf18; UBCE7IP3
Summary
The protein encoded by this gene is similar to mouse UIP28/UbcM4 interacting protein. Alternative splicing has been observed at this locus, resulting in distinct isoforms. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in spleen (RPKM 15.0), prostate (RPKM 9.4) and 25 other tissues See more
Orthologs

Genomic context

See RBCK1 in Genome Data Viewer
Location:
20p13
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 20 NC_000020.11 (408050..432139)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (388696..411610)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929937 Neighboring gene neurensin 2 Neighboring gene tribbles pseudokinase 3 Neighboring gene TBC1 domain family member 20 Neighboring gene casein kinase 2 alpha 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Antigen processing: Ubiquitination & Proteasome degradation, organism-specific biosystem (from REACTOME)
    Antigen processing: Ubiquitination & Proteasome degradation, organism-specific biosystemIntracellular foreign or aberrant host proteins are cleaved into peptide fragments of a precise size, such that they can be loaded on to class I MHC molecules and presented externally to cytotoxic T ...
  • Class I MHC mediated antigen processing & presentation, organism-specific biosystem (from REACTOME)
    Class I MHC mediated antigen processing & presentation, organism-specific biosystemMajor histocompatibility complex (MHC) class I molecules play an important role in cell mediated immunity by reporting on intracellular events such as viral infection, the presence of intracellular b...
  • Death Receptor Signalling, organism-specific biosystem (from REACTOME)
    Death Receptor Signalling, organism-specific biosystemThe death receptors, all cell-surface receptors, begin the process of caspase activation. The common feature of these type 1 transmembrane proteins is the "death-domain" a conserved cytoplasmic motif...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • NOD-like receptor signaling pathway, organism-specific biosystem (from KEGG)
    NOD-like receptor signaling pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting various pathogens and generating innate immune responses. The intracellular NOD-like receptor (NLR) family contains mo...
  • NOD-like receptor signaling pathway, conserved biosystem (from KEGG)
    NOD-like receptor signaling pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting various pathogens and generating innate immune responses. The intracellular NOD-like receptor (NLR) family contains mo...
  • Regulation of TNFR1 signaling, organism-specific biosystem (from REACTOME)
    Regulation of TNFR1 signaling, organism-specific biosystemTumor necrosis factor-alpha (TNFalpha) is an inflammatory cytokine, that activates either cell survival (e.g.,inflammation, proliferation) or cell death upon association with TNF receptor 1 (TNFR1). ...
  • Regulation of toll-like receptor signaling pathway, organism-specific biosystem (from WikiPathways)
    Regulation of toll-like receptor signaling pathway, organism-specific biosystem
    Regulation of toll-like receptor signaling pathway
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • TNF signaling, organism-specific biosystem (from REACTOME)
    TNF signaling, organism-specific biosystemThe inflammatory cytokine tumor necrosis factor alpha (TNF-alpha) is expressed in immune and nonimmune cell types including macrophages, T cells, mast cells, granulocytes, natural killer (NK) cells, ...
  • TNFR1-induced NFkappaB signaling pathway, organism-specific biosystem (from REACTOME)
    TNFR1-induced NFkappaB signaling pathway, organism-specific biosystemActivation of tumor necrosis factor receptor 1 (TNFR1) can trigger multiple signal transduction pathways to induce inflammation, cell proliferation, survival or cell death (Ward C et al. 1999; Michea...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin binding IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin-protein transferase activity EXP
Inferred from Experiment
more info
PubMed 
ubiquitin-protein transferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin-protein transferase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
I-kappaB kinase/NF-kappaB signaling TAS
Traceable Author Statement
more info
 
T cell receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of NF-kappaB transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of necroptotic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of I-kappaB kinase/NF-kappaB signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of I-kappaB kinase/NF-kappaB signaling IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of NF-kappaB transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of NIK/NF-kappaB signaling IEA
Inferred from Electronic Annotation
more info
 
positive regulation of extrinsic apoptotic signaling pathway IEA
Inferred from Electronic Annotation
more info
 
proteasome-mediated ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proteasome-mediated ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein linear polyubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein linear polyubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein polyubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein polyubiquitination TAS
Traceable Author Statement
more info
 
regulation of tumor necrosis factor-mediated signaling pathway TAS
Traceable Author Statement
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
LUBAC complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
LUBAC complex IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
ranBP-type and C3HC4-type zinc finger-containing protein 1
Names
HBV-associated factor 4
RBCC protein interacting with PKC1
RING finger protein 54
RING-type E3 ubiquitin transferase HOIL-1
heme-oxidized IRP2 ubiquitin ligase 1
hepatitis B virus X-associated protein 4
ubiquitin conjugating enzyme 7 interacting protein 3
NP_001310885.1
NP_001310887.1
NP_001310889.1
NP_006453.1
NP_112506.2
XP_005260702.1
XP_011527439.1
XP_011527440.1
XP_011527441.1
XP_011527442.1
XP_016883083.1
XP_016883084.1

NCBI Reference Sequences (RefSeq)

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_033233.1 RefSeqGene

    Range
    5001..27902
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001323956.1NP_001310885.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL121747, AW293635
    Consensus CDS
    CCDS82588.1
    UniProtKB/TrEMBL
    A6PVK0
    Related
    ENSP00000491402.1, ENST00000640614.1
    Conserved Domains (1) summary
    cl17238
    Location:136162
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
  2. NM_001323958.1NP_001310887.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL121747, AW293635, BC000983, BC014116
    Consensus CDS
    CCDS82588.1
    UniProtKB/TrEMBL
    A6PVK0
    Related
    ENSP00000371616.2, OTTHUMP00000196665, ENST00000382181.2, OTTHUMT00000077457
    Conserved Domains (1) summary
    cl17238
    Location:136162
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
  3. NM_001323960.1NP_001310889.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AK309414, BC014116, BC016301
    Consensus CDS
    CCDS82587.1
    UniProtKB/TrEMBL
    A6PVJ6
    Related
    ENSP00000417173.1, OTTHUMP00000196662, ENST00000475269.5, OTTHUMT00000077452
  4. NM_006462.5NP_006453.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_006453.1

    Status: REVIEWED

    Source sequence(s)
    AB107766, AL121747, AW293635, BC014116
    Consensus CDS
    CCDS12998.1
    UniProtKB/Swiss-Prot
    Q9BYM8
    Related
    ENSP00000254960.5, OTTHUMP00000029921, ENST00000353660.7, OTTHUMT00000077460
    Conserved Domains (5) summary
    cd01799
    Location:1589
    Hoil1_N; Ubiquitin-like domain of HOIL1
    smart00547
    Location:155175
    ZnF_RBZ; Zinc finger domain
    sd00029
    Location:155174
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam01485
    Location:328362
    IBR; IBR domain, a half RING-finger domain
    cd16633
    Location:236290
    mRING-HC-C3HC3D_RBR_HOIL1; Modified RING finger, HC subclass (C3HC3D-type), found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins
  5. NM_031229.3NP_112506.2  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_112506.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes the longest isoform (2).
    Source sequence(s)
    AL121747, AW293635, BC014116, BC015219
    Consensus CDS
    CCDS13000.2
    UniProtKB/Swiss-Prot
    Q9BYM8
    Related
    ENSP00000348632.5, OTTHUMP00000029922, ENST00000356286.9, OTTHUMT00000077461
    Conserved Domains (5) summary
    cd01799
    Location:57131
    Hoil1_N; Ubiquitin-like domain of HOIL1
    smart00547
    Location:197217
    ZnF_RBZ; Zinc finger domain
    sd00029
    Location:197216
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam01485
    Location:370404
    IBR; IBR domain, a half RING-finger domain
    cd16633
    Location:278332
    mRING-HC-C3HC3D_RBR_HOIL1; Modified RING finger, HC subclass (C3HC3D-type), found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins

RNA

  1. NR_136659.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL121747, AW293635, BC014116

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p12 Primary Assembly

    Range
    408050..432139
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011529137.2XP_011527439.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X1

    Conserved Domains (5) summary
    cd01799
    Location:115189
    Hoil1_N; Ubiquitin-like domain of HOIL1
    smart00547
    Location:255275
    ZnF_RBZ; Zinc finger domain
    sd00029
    Location:255274
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam01485
    Location:428462
    IBR; IBR domain, a half RING-finger domain
    pfam13445
    Location:340382
    zf-RING_UBOX; RING-type zinc-finger
  2. XM_005260645.2XP_005260702.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X3

    Conserved Domains (5) summary
    cd01799
    Location:74148
    Hoil1_N; Ubiquitin-like domain of HOIL1
    smart00547
    Location:214234
    ZnF_RBZ; Zinc finger domain
    sd00029
    Location:214233
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam01485
    Location:387421
    IBR; IBR domain, a half RING-finger domain
    pfam13445
    Location:299341
    zf-RING_UBOX; RING-type zinc-finger
  3. XM_017027594.2XP_016883083.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X6

    UniProtKB/TrEMBL
    A6PVK0
    Conserved Domains (1) summary
    cl17238
    Location:136162
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
  4. XM_011529138.1XP_011527440.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X2

    Conserved Domains (5) summary
    cd01799
    Location:98172
    Hoil1_N; Ubiquitin-like domain of HOIL1
    smart00547
    Location:238258
    ZnF_RBZ; Zinc finger domain
    sd00029
    Location:238257
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam01485
    Location:411445
    IBR; IBR domain, a half RING-finger domain
    pfam13445
    Location:323365
    zf-RING_UBOX; RING-type zinc-finger
  5. XM_011529139.3XP_011527441.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X4

    Conserved Domains (5) summary
    cd01799
    Location:115189
    Hoil1_N; Ubiquitin-like domain of HOIL1
    smart00547
    Location:255275
    ZnF_RBZ; Zinc finger domain
    sd00029
    Location:255274
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
    pfam01485
    Location:406462
    IBR; IBR domain, a half RING-finger domain
    pfam13445
    Location:340382
    zf-RING_UBOX; RING-type zinc-finger
  6. XM_011529140.2XP_011527442.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X5

    Conserved Domains (3) summary
    cd01799
    Location:115189
    Hoil1_N; Ubiquitin-like domain of HOIL1
    smart00547
    Location:255275
    ZnF_RBZ; Zinc finger domain
    sd00029
    Location:255274
    zf-RanBP2; RanBP2-type Zn finger [structural motif]
  7. XM_017027595.1XP_016883084.1  ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X6

    UniProtKB/TrEMBL
    A6PVK0
    Conserved Domains (1) summary
    cl17238
    Location:136162
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

RNA

  1. XR_001754130.2 RNA Sequence

  2. XR_937029.3 RNA Sequence

  3. XR_001754131.1 RNA Sequence

    Related
    ENST00000415942.5, OTTHUMT00000077462

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_031227.1: Suppressed sequence

    Description
    NM_031227.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
  2. NM_031228.1: Suppressed sequence

    Description
    NM_031228.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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