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    RNF103 ring finger protein 103 [ Homo sapiens (human) ]

    Gene ID: 7844, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RNF103provided by HGNC
    Official Full Name
    ring finger protein 103provided by HGNC
    Primary source
    HGNC:HGNC:12859
    See related
    Ensembl:ENSG00000239305 MIM:602507; AllianceGenome:HGNC:12859
    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
    KF1; KF-1; HKF-1; ZFP103; ZFP-103
    Summary
    The protein encoded by this gene contains a RING-H2 finger, a motif known to be involved in protein-protein and protein-DNA interactions. This gene is highly expressed in normal cerebellum, but not in the cerebral cortex. The expression of the rat counterpart in the frontal cortex and hippocampus was shown to be induced by elctroconvulsive treatment (ECT) as well as chronic antidepressant treatment, suggesting that this gene may be a molecular target for ECT and antidepressants. The protein is a ubiquitin ligase that functions in the endoplasmic reticulum-associated degradation pathway. Alternative splicing of this gene results in multiple transcript variants. Read-through transcription also exists between this gene and the downstream CHMP3 (charged multivesicular body protein 3) gene. [provided by RefSeq, Oct 2011]
    Expression
    Ubiquitous expression in bone marrow (RPKM 15.1), small intestine (RPKM 12.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RNF103 in Genome Data Viewer
    Location:
    2p11.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (86603393..86623877, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (86605396..86625879, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (86830516..86851000, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:86667563-86668106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11713 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16161 Neighboring gene lysine demethylase 3A Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:86708929-86710128 Neighboring gene MPRA-validated peak3779 silencer Neighboring gene RNF103-CHMP3 readthrough Neighboring gene RNA, U6 small nuclear 640, pseudogene Neighboring gene charged multivesicular body protein 3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_59439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16164 Neighboring gene Sharpr-MPRA regulatory region 1991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16163 Neighboring gene CHMP3 and RNF103 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11717 Neighboring gene Sharpr-MPRA regulatory region 3990 Neighboring gene uncharacterized LOC124907853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86859935-86860458 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:86921806-86923005 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:86946607-86947140 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:86947334-86947492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86952106-86952606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86952607-86953107 Neighboring gene required for meiotic nuclear division 5 homolog A

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Induction of kf-1 after repeated electroconvulsive treatment and chronic antidepressant treatment in rat frontal cortex and hippocampus. Nishioka G, et al. J Neural Transm (Vienna), 2003 Mar. PMID 12658376
    2. Expression and evaluation of RING finger proteins. Yang Y, et al. Methods Enzymol, 2005. PMID 16275323
    3. Cloning of human and mouse cDNAs encoding novel zinc finger proteins expressed in cerebellum and hippocampus. Yasojima K, et al. Biochem Biophys Res Commun, 1997 Feb 13. PMID 9070305
    4. Identification of a novel gene with RING-H2 finger motif induced after chronic antidepressant treatment in rat brain. Yamada M, et al. Biochem Biophys Res Commun, 2000 Nov 11. PMID 11071867
    5. Ubiquitin ligase Kf-1 is involved in the endoplasmic reticulum-associated degradation pathway. Maruyama Y, et al. Biochem Biophys Res Commun, 2008 Oct 3. PMID 18675248

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Analysis reveals that the main determinants of selectivity between ubiquitin ligases RNF103 and E2 ubiquitin-conjugating enzymes resides on ring domains, rather than on the E2s.
      Title: Analysis of electrostatic contributions to the selectivity of interactions between RING-finger domains and ubiquitin-conjugating enzymes.
    2. Kf-1 is an ER ubiquitin ligase involved in the endoplasmic reticulum-associated degradation pathway.
      Title: Ubiquitin ligase Kf-1 is involved in the endoplasmic reticulum-associated degradation pathway.
    Submit: New GeneRIF Correction

    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

    Readthrough RNF103-CHMP3

    Readthrough gene: RNF103-CHMP3, Included gene: CHMP3

    Homology

    Clone Names

    • MGC41857, MGC102815

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 TAS
    Traceable Author Statement
    more info
    		  
    enables ubiquitin-protein transferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ERAD pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in central nervous system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in endoplasmic reticulum mannose trimming TAS
    Traceable Author Statement
    more info
    		  
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum quality control compartment IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase RNF103
    Names
    RING-type E3 ubiquitin transferase RNF103
    zinc finger protein 103 homolog
    zinc finger protein expressed in cerebellum
    NP_001185880.1
    NP_001185881.1
    NP_005658.1

    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_001198951.1 → NP_001185880.1  E3 ubiquitin-protein ligase RNF103 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      BC110333, BQ018198, DA816879
      UniProtKB/Swiss-Prot
      O00237
      Conserved Domains (1) summary
      cd00162
      Location:616 → 659
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

    2. NM_001198952.2 → NP_001185881.1  E3 ubiquitin-protein ligase RNF103 isoform 3

      See identical proteins and their annotated locations for NP_001185881.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains alternate 3' exon structure and uses an early stop codon, compared to variant 1. The encoded isoform (3) is shorter at the C-terminus, compared to isoform 1.
      Source sequence(s)
      AI150469, AW964704, BC022477, BC035053, CA312650, DA816879
      UniProtKB/Swiss-Prot
      O00237

    3. NM_005667.4 → NP_005658.1  E3 ubiquitin-protein ligase RNF103 isoform 1

      See identical proteins and their annotated locations for NP_005658.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AW964704, BC035053, BC110333, DA816879
      Consensus CDS
      CCDS33237.1
      UniProtKB/Swiss-Prot
      A6NFV6, B2RAG4, O00237, Q53SU6, Q8IVB9
      Related
      ENSP00000237455.4, ENST00000237455.5
      Conserved Domains (1) summary
      cd00162
      Location:620 → 663
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      86603393..86623877 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      86605396..86625879 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O00237.1 GenPept UniProtKB/Swiss-Prot:O00237

    Gene LinkOut

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