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

Summary

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

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_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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

General gene information

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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

EC 2.3.2.27

XP_006230281.1

EC 2.3.2.27

XP_038958366.1

EC 2.3.2.27

XP_038958376.1

EC 2.3.2.27

XP_063138489.1

EC 2.3.2.27

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)

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

NC_086019.1 Reference GRCr8

Range

191632988..191649231

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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