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Rnf40 ring finger protein 40 [ Rattus norvegicus (Norway rat) ]

Gene ID: 266712, updated on 2-Nov-2024

Summary

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Official Symbol
Rnf40provided by RGD
Official Full Name
ring finger protein 40provided by RGD
Primary source
RGD:628638
See related
EnsemblRapid:ENSRNOG00000018840 AllianceGenome:RGD:628638
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Enables syntaxin-1 binding activity; ubiquitin conjugating enzyme binding activity; and ubiquitin-protein transferase activity. Involved in positive regulation of protein metabolic process; response to peptide hormone; and ubiquitin-dependent protein catabolic process. Part of protein-containing complex. Biomarker of nephrogenic diabetes insipidus. Orthologous to human RNF40 (ring finger protein 40). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Kidney (RPKM 147.4), Thymus (RPKM 137.9) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Rnf40 in Genome Data Viewer
Location:
1q37
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (191632988..191649231)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (182202475..182217899)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (199037472..199052823)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene Snf2-related CREBBP activator protein Neighboring gene transmembrane protein 265 Neighboring gene phosphorylase kinase catalytic subunit gamma 2 Neighboring gene cilia and flagella associated protein 119 Neighboring gene zinc finger protein 629 Neighboring gene 5S ribosomal RNA Neighboring gene BAF chromatin remodeling complex subunit BCL7C Neighboring gene microRNA 762

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. E3 ubiquitin-protein ligases in rat kidney collecting duct: response to vasopressin stimulation and withdrawal. Lee YJ, et al. Am J Physiol Renal Physiol, 2011 Oct. PMID 21734099
  2. The ATM signaling network in development and disease. Stracker TH, et al. Front Genet, 2013. PMID 23532176, Free PMC Article
  3. RBP95, a novel leucine zipper protein, binds to the retinoblastoma protein. Wen H, et al. Biochem Biophys Res Commun, 2000 Aug 18. PMID 10944455
  4. Staring, a novel E3 ubiquitin-protein ligase that targets syntaxin 1 for degradation. Chin LS, et al. J Biol Chem, 2002 Sep 20. PMID 12121982
  5. CDK9 directs H2B monoubiquitination and controls replication-dependent histone mRNA 3'-end processing. Pirngruber J, et al. EMBO Rep, 2009 Aug. PMID 19575011, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. a novel E3 ubiquitin-protein ligase that targets syntaxin 1 for degradation
    Title: Staring, a novel E3 ubiquitin-protein ligase that targets syntaxin 1 for degradation.
Submit: New GeneRIF Correction

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables mRNA 3'-UTR binding IEA
Inferred from Electronic Annotation
more info
  
enables mRNA 3'-UTR binding ISO
Inferred from Sequence Orthology
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
  
enables syntaxin-1 binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin conjugating enzyme binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin protein ligase binding IEA
Inferred from Electronic Annotation
more info
  
enables ubiquitin protein ligase binding ISO
Inferred from Sequence Orthology
more info
  
enables ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin-protein transferase activity IEA
Inferred from Electronic Annotation
more info
  
contributes_to ubiquitin-protein transferase activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of proteasomal protein catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of protein polyubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
NOT involved_in regulation of mitotic cell cycle ISO
Inferred from Sequence Orthology
more info
  
involved_in response to peptide hormone IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of HULC complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of HULC complex IEA
Inferred from Electronic Annotation
more info
  
part_of HULC complex ISO
Inferred from Sequence Orthology
more info
  
part_of HULC complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of ubiquitin ligase complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
E3 ubiquitin-protein ligase BRE1B
Names
BRE1-B
RING-type E3 ubiquitin transferase BRE1B
protein staring
ring finger protein 40, E3 ubiquitin protein ligase
staring protein
syntaxin-1-interacting RING finger protein
NP_703201.1
XP_006230281.1
XP_038958366.1
XP_038958376.1
XP_063138489.1

NCBI Reference Sequences (RefSeq)

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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_153471.1 → NP_703201.1  E3 ubiquitin-protein ligase BRE1B

    See identical proteins and their annotated locations for NP_703201.1

    Status: PROVISIONAL

    Source sequence(s)
    AF352815
    UniProtKB/Swiss-Prot
    Q8CJB9
    UniProtKB/TrEMBL
    A6I9S2, A6I9S3
    Related
    ENSRNOP00000094962.1, ENSRNOT00000098677.2
    Conserved Domains (2) summary
    TIGR02168
    Location:201 → 921
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    cd16815
    Location:946 → 1000
    RING-HC_RNF40; RING finger, HC subclass, found in RING finger protein 40 (RNF40)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086019.1 Reference GRCr8

    Range
    191632988..191649231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063282419.1 → XP_063138489.1  E3 ubiquitin-protein ligase BRE1B isoform X3

  2. XM_039102438.2 → XP_038958366.1  E3 ubiquitin-protein ligase BRE1B isoform X2

    UniProtKB/TrEMBL
    A6I9S1
    Conserved Domains (1) summary
    TIGR02168
    Location:225 → 867
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type

  3. XM_006230219.5 → XP_006230281.1  E3 ubiquitin-protein ligase BRE1B isoform X1

    UniProtKB/TrEMBL
    A0A8L2UK73, A6I9S2
    Related
    ENSRNOP00000025500.2, ENSRNOT00000025499.4
    Conserved Domains (3) summary
    cd00162
    Location:953 → 996
    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 ...
    TIGR02168
    Location:225 → 926
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam08647
    Location:760 → 854
    BRE1; BRE1 E3 ubiquitin ligase

  4. XM_039102448.2 → XP_038958376.1  E3 ubiquitin-protein ligase BRE1B isoform X4

    UniProtKB/TrEMBL
    A6I9S4
    Conserved Domains (3) summary
    PTZ00121
    Location:300 → 593
    PTZ00121; MAEBL; Provisional
    TIGR02168
    Location:1 → 587
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    cd16815
    Location:612 → 666
    RING-HC_RNF40; RING finger, HC subclass, found in RING finger protein 40 (RNF40)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8CJB9.1 GenPept UniProtKB/Swiss-Prot:Q8CJB9

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