Rffl ring finger and FYVE-like domain containing E3 ubiquitin protein ligase [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Rfflprovided by RGD
Official Full Name: ring finger and FYVE-like domain containing E3 ubiquitin protein ligaseprovided by RGD
Primary source: RGD:727916
See related: EnsemblRapid:ENSRNOG00000007596 AllianceGenome:RGD:727916
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable enzyme binding activity; p53 binding activity; and ubiquitin protein ligase activity. Predicted to be involved in several processes, including negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis; negative regulation of signal transduction; and protein K48-linked ubiquitination. Predicted to act upstream of or within intracellular protein transport. Predicted to be located in endosome membrane. Predicted to be active in cytoplasm and plasma membrane. Biomarker of hypertension. Orthologous to human RFFL (ring finger and FYVE like domain containing E3 ubiquitin protein ligase). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 109.6), Kidney (RPKM 84.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q26

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (68238273..68301225, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (67740711..67803669, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (70157621..70220618, complement)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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 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?

Targeted disruption of the rat Rffl-lnc1 locus caused aberrant, short QT-intervals and elevated blood pressure. Further, to specifically examine the significance of the 19bp polymorphism within the Rffl-lnc1 locus, a CRISPR/Cas9 based targeted knock-in rescue model was constructed by inserting the 19bp into the strain which contained the deletion polymorphism.
Title: Positional cloning of quantitative trait nucleotides for blood pressure and cardiac QT-interval by targeted CRISPR/Cas9 editing of a novel long non-coding RNA.
our study provides evidence to suggest that early perturbations in endocytic recycling caused by the overexpression of Rffl is a novel physiological mechanism potentially underlying the development of hypertension.
Title: Augmented rififylin is a risk factor linked to aberrant cardiomyocyte function, short-QT interval and hypertension.
identified two novel Ub ligases, Momo and Sakura, carrying double zinc finger motif and RING finger domain in rat brain; Sakura expression is more widely detected in the brain white matter as well as in many peripheral organs
Title: A palmitoylated RING finger ubiquitin ligase and its homologue in the brain membranes.

Submit: New GeneRIF Correction

General gene information

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Markers

D10Got87 (e-PCR)
- UniSTS:111672

D10Chm171 (e-PCR)
- UniSTS:518384

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables p53 binding	IEA Inferred from Electronic Annotation more info
enables p53 binding	ISO Inferred from Sequence Orthology more info
enables protease binding	IEA Inferred from Electronic Annotation more info
enables protease binding	ISO Inferred from Sequence Orthology more info
enables protein kinase binding	IEA Inferred from Electronic Annotation more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase activity	ISS Inferred from Sequence or Structural Similarity 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

Process	Evidence Code	Pubs
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within intracellular protein transport	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of signal transduction by p53 class mediator	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of signal transduction by p53 class mediator	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of signal transduction by p53 class mediator	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of tumor necrosis factor-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of tumor necrosis factor-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of tumor necrosis factor-mediated signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein K48-linked ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein K48-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein K48-linked ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of fibroblast migration	ISO Inferred from Sequence Orthology more info
involved_in regulation of fibroblast migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
NOT located_in Golgi membrane	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasmic vesicle	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in endosome membrane	ISO Inferred from Sequence Orthology more info
located_in endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
NOT located_in lysosome	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in recycling endosome membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase rififylin

Names: FYVE-RING finger protein Sakura; RING finger and FYVE-like domain-containing protein 1; RING finger protein SAKURA; RING-type E3 ubiquitin transferase rififylin; fring; ring finger and FYVE like domain containing protein; ring finger and FYVE-like domain containing 1

NP_001004068.1

EC 2.3.2.27

NP_001386503.1

EC 2.3.2.27

XP_006247031.1

EC 2.3.2.27

XP_006247032.1

EC 2.3.2.27

XP_006247036.1

EC 2.3.2.27

XP_006247039.1

EC 2.3.2.27

XP_038941249.1

EC 2.3.2.27

XP_038941251.1

EC 2.3.2.27

XP_063124568.1

EC 2.3.2.27

XP_063124569.1

EC 2.3.2.27

XP_063124570.1

EC 2.3.2.27

XP_063124571.1

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_001004068.2 → NP_001004068.1 E3 ubiquitin-protein ligase rififylin isoform 2

See identical proteins and their annotated locations for NP_001004068.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A0A8L2QM30

Related

ENSRNOP00000067950.1, ENSRNOT00000076598.4

Conserved Domains (2) summary

cd15770
Location:44 → 92

FYVE_CARP2; FYVE-like domain found in caspase regulator CARP2 and similar proteins

pfam13920
Location:283 → 327

zf-C3HC4_3; Zinc finger, C3HC4 type (RING finger)
NM_001399574.1 → NP_001386503.1 E3 ubiquitin-protein ligase rififylin isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

Q6AY29, Q8CIN9

UniProtKB/TrEMBL

A6HHE4

Related

ENSRNOP00000045245.4, ENSRNOT00000041389.6

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_086028.1 Reference GRCr8

Range

68238273..68301225 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063268501.1 → XP_063124571.1 E3 ubiquitin-protein ligase rififylin isoform X7
XM_006246974.5 → XP_006247036.1 E3 ubiquitin-protein ligase rififylin isoform X5

See identical proteins and their annotated locations for XP_006247036.1

UniProtKB/TrEMBL

A0A096MJC6, A0A8L2QM30

Related

ENSRNOP00000108638.1, ENSRNOT00000170731.1

Conserved Domains (2) summary

cd16500
Location:315 → 353

RING-HC_CARP; RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein CARP-1, CARP-2 and similar proteins

cl28890
Location:44 → 93

FYVE_like_SF; FYVE domain like superfamily
XM_063268500.1 → XP_063124570.1 E3 ubiquitin-protein ligase rififylin isoform X6

UniProtKB/Swiss-Prot

Q6AY29, Q8CIN9

UniProtKB/TrEMBL

A6HHE4
XM_006246977.5 → XP_006247039.1 E3 ubiquitin-protein ligase rififylin isoform X5

See identical proteins and their annotated locations for XP_006247039.1

UniProtKB/TrEMBL

A0A096MJC6, A0A8L2QM30

Conserved Domains (2) summary

cd16500
Location:315 → 353

RING-HC_CARP; RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein CARP-1, CARP-2 and similar proteins

cl28890
Location:44 → 93

FYVE_like_SF; FYVE domain like superfamily
XM_063268498.1 → XP_063124568.1 E3 ubiquitin-protein ligase rififylin isoform X3
XM_006246969.4 → XP_006247031.1 E3 ubiquitin-protein ligase rififylin isoform X1

See identical proteins and their annotated locations for XP_006247031.1

UniProtKB/TrEMBL

A0A8L2QM30

Conserved Domains (3) summary

pfam03873
Location:193 → 242

RseA_C; Anti sigma-E protein RseA, C-terminal domain

pfam13920
Location:347 → 391

zf-C3HC4_3; Zinc finger, C3HC4 type (RING finger)

cl22851
Location:79 → 128

PHD_SF; PHD finger superfamily
XM_039085321.2 → XP_038941249.1 E3 ubiquitin-protein ligase rififylin isoform X5

UniProtKB/TrEMBL

A0A096MJC6, A0A8L2QM30

Conserved Domains (2) summary

cd16500
Location:315 → 353

RING-HC_CARP; RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein CARP-1, CARP-2 and similar proteins

cl28890
Location:44 → 93

FYVE_like_SF; FYVE domain like superfamily
XM_006246970.4 → XP_006247032.1 E3 ubiquitin-protein ligase rififylin isoform X2

UniProtKB/TrEMBL

A0A8L2QM30, A0A8L2QZU3

Related

ENSRNOP00000068131.2, ENSRNOT00000076596.4

Conserved Domains (3) summary

cd15770
Location:79 → 127

FYVE_CARP2; FYVE-like domain found in caspase regulator CARP2 and similar proteins

pfam03873
Location:192 → 241

RseA_C; Anti sigma-E protein RseA, C-terminal domain

pfam13920
Location:346 → 390

zf-C3HC4_3; Zinc finger, C3HC4 type (RING finger)
XM_063268499.1 → XP_063124569.1 E3 ubiquitin-protein ligase rififylin isoform X4
XM_039085323.2 → XP_038941251.1 E3 ubiquitin-protein ligase rififylin isoform X5

UniProtKB/TrEMBL

A0A096MJC6, A0A8L2QM30

Conserved Domains (2) summary

cd16500
Location:315 → 353

RING-HC_CARP; RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein CARP-1, CARP-2 and similar proteins

cl28890
Location:44 → 93

FYVE_like_SF; FYVE domain like superfamily