Rufy3 RUN and FYVE domain containing 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rufy3provided by MGI
Official Full Name: RUN and FYVE domain containing 3provided by MGI
Primary source: MGI:MGI:106484
See related: Ensembl:ENSMUSG00000029291 AllianceGenome:MGI:106484
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Ripx; Rpipx; D5Bwg0860e; 2810428M05Rik; 6330416M07Rik
Summary: Involved in several processes, including positive regulation of axon extension; positive regulation of intracellular protein transport; and regulation of establishment of cell polarity. Acts upstream of or within positive regulation of axonogenesis. Located in dendrite; growth cone; and perikaryon. Is expressed in several structures, including alimentary system; eye; genitourinary system; nervous system; and skin. Orthologous to human RUFY3 (RUN and FYVE domain containing 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in CNS E18 (RPKM 20.6), whole brain E14.5 (RPKM 18.1) and 18 other tissues See more
Orthologs: human all
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Genomic context

Location:: 5 E1; 5 43.77 cM

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	5	NC_000071.7 (88711305..88799276)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	5	NC_000071.6 (88564505..88651417)

Chromosome 5 - NC_000071.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RUFY3, a neuronally enriched protein, is essential for caspase-mediated degeneration of TRKA+ sensory axons in vitro and in vivo. Deletion of Rufy3 protects axons from degeneration, even in the presence of activated CASP3 . Dephosphorylation of RUFY3 at residue S34 appears required for axon degeneration.
Title: Neuronally Enriched RUFY3 Is Required for Caspase-Mediated Axon Degeneration.
Rufy3 is a physiological adapter for Rap2 and activates Tiam2/STEF in glycoprotein M6A-regulated neuronal polarity and axon growth.
Title: Rufy3 is an adapter protein for small GTPases that activates a Rac guanine nucleotide exchange factor to control neuronal polarity.
We propose that Rufy3 may control mouse neuron axon development
Title: Rufy3, a protein specifically expressed in neurons, interacts with actin-bundling protein Fascin to control the growth of axons.
the putative Rap2 binding site of the RPIPx RUN domain interacts with the extended segment in a segment-swapping manner
Title: Crystal structure of the RUN domain of the RAP2-interacting protein x.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (4) 1 citation
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW538594 (e-PCR)
- UniSTS:185630

D17936 (e-PCR)
- UniSTS:124744

RH125096 (e-PCR)
- UniSTS:161918

21.MMHAP64FLG3.seq (e-PCR)
- UniSTS:123531

D5Bwg0860e (e-PCR), detects polymorphism
- UniSTS:142538

NoName (e-PCR)
- UniSTS:235210

AW455998 (e-PCR)
- UniSTS:179194

Homology

Homologs of the Rufy3 gene: The Rufy3 gene is conserved in human, chimpanzee, dog, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 486 organisms have orthologs with human gene Rufy3
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in actin filament organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of axonogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of axon extension	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of axonogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of intracellular protein transport	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of axonogenesis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within regulation of axonogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of establishment of cell polarity	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in cell junction	IEA Inferred from Electronic Annotation more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
is_active_in dendrite	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in dendrite	ISO Inferred from Sequence Orthology more info
located_in filopodium	ISO Inferred from Sequence Orthology more info
located_in growth cone	IDA Inferred from Direct Assay more info	PubMed
located_in growth cone	ISO Inferred from Sequence Orthology more info
located_in lamellipodium	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in neuronal cell body	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in perikaryon	IDA Inferred from Direct Assay more info	PubMed
located_in perikaryon	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: protein RUFY3

Names: rap2 interacting protein x; singar; singar1; single axon-regulated protein 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)

NM_001289774.1 → NP_001276703.1 protein RUFY3 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC121541, AK160820, BP765560

Consensus CDS

CCDS80324.1

UniProtKB/TrEMBL

A0A0G2JFT8

Related

ENSMUSP00000143302.2, ENSMUST00000198965.5

Conserved Domains (5) summary

cd15744
Location:611 → 657

FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins

pfam01442
Location:324 → 497

Apolipoprotein; Apolipoprotein A1/A4/E domain

pfam02759
Location:153 → 276

RUN; RUN domain

pfam10212
Location:323 → 372

TTKRSYEDQ; Predicted coiled-coil domain-containing protein

cl23720
Location:390 → 499

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
NM_001289775.1 → NP_001276704.1 protein RUFY3 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks several exons in the 3' coding region and contains an alternate 3' terminal exon, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AK160820, BM898740

Consensus CDS

CCDS80323.1

UniProtKB/Swiss-Prot

Q9D394

Related

ENSMUSP00000143770.2, ENSMUST00000196894.5

Conserved Domains (4) summary

pfam01442
Location:324 → 496

Apolipoprotein; Apolipoprotein A1/A4/E domain

pfam02759
Location:153 → 276

RUN; RUN domain

pfam10212
Location:323 → 372

TTKRSYEDQ; Predicted coiled-coil domain-containing protein

cl23720
Location:390 → 518

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
NM_001289776.2 → NP_001276705.1 protein RUFY3 isoform 3

See identical proteins and their annotated locations for NP_001276705.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region, initiates translation at an alternate start codon and contains an alternate 3' terminal exon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which is shorter and has distinct N- and C-termini, compared to isoform 1.

Source sequence(s)

AC121541

Consensus CDS

CCDS80325.1

UniProtKB/Swiss-Prot

Q9D394

Related

ENSMUSP00000143209.2, ENSMUST00000196686.2

Conserved Domains (2) summary

pfam02759
Location:121 → 244

RUN; RUN domain

pfam10212
Location:291 → 340

TTKRSYEDQ; Predicted coiled-coil domain-containing protein
NM_001289777.2 → NP_001276706.1 protein RUFY3 isoform 3

See identical proteins and their annotated locations for NP_001276706.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region, initiates translation at an alternate start codon and contains an alternate 3' terminal exon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which is shorter and has distinct N- and C-termini, compared to isoform 1.

Source sequence(s)

AC121541

Consensus CDS

CCDS80325.1

UniProtKB/Swiss-Prot

Q9D394

Related

ENSMUSP00000143115.2, ENSMUST00000199312.5

Conserved Domains (2) summary

pfam02759
Location:121 → 244

RUN; RUN domain

pfam10212
Location:291 → 340

TTKRSYEDQ; Predicted coiled-coil domain-containing protein
NM_001359208.2 → NP_001346137.1 protein RUFY3 isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (6) differs in the 5' UTR and 5' coding region, initiates translation at an alternate start codon and contains an alternate 3' terminal exon, compared to variant 1. It encodes isoform 4, which is shorter and has distinct N- and C-termini, compared to isoform 1. Variants 5 and 6 both encode the same isoform (4).

Source sequence(s)

AC121541

Consensus CDS

CCDS19403.1

UniProtKB/Swiss-Prot

Q8VD10

Conserved Domains (2) summary

pfam02759
Location:103 → 224

RUN; RUN domain

cl25732
Location:258 → 464

SMC_N; RecF/RecN/SMC N terminal domain
NM_001359209.2 → NP_001346138.1 protein RUFY3 isoform 5

Status: VALIDATED

Description

Transcript Variant: This variant (7) differs in the 5' UTR and 5' coding region and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 5, which is shorter and has a distinct N-terminus, compared to isoform 1.

Source sequence(s)

AC121541

Conserved Domains (3) summary

TIGR02168
Location:243 → 502

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd15744
Location:561 → 607

FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins

pfam02759
Location:103 → 224

RUN; RUN domain
NM_027530.4 → NP_081806.1 protein RUFY3 isoform 4

See identical proteins and their annotated locations for NP_081806.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and 5' coding region, initiates translation at an alternate start codon and contains an alternate 3' terminal exon, compared to variant 1. It encodes isoform 4, which is shorter and has distinct N- and C-termini, compared to isoform 1. Variants 5 and 6 both encode the same isoform (4).

Source sequence(s)

AC121541

Consensus CDS

CCDS19403.1

UniProtKB/Swiss-Prot

Q8VD10, Q9D394

Related

ENSMUSP00000031229.7, ENSMUST00000031229.11

Conserved Domains (2) summary

pfam02759
Location:103 → 224

RUN; RUN domain

cl25732
Location:258 → 464

SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000071.7 Reference GRCm39 C57BL/6J

Range

88711305..88799276

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006535115.5 → XP_006535178.1 protein RUFY3 isoform X5

See identical proteins and their annotated locations for XP_006535178.1

Conserved Domains (3) summary

TIGR02168
Location:179 → 438

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd15744
Location:497 → 543

FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins

pfam02759
Location:39 → 160

RUN; RUN domain
XM_036165294.1 → XP_036021187.1 protein RUFY3 isoform X7

Conserved Domains (2) summary

COG1196
Location:192 → 400

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

pfam02759
Location:39 → 160

RUN; RUN domain
XM_006535109.4 → XP_006535172.1 protein RUFY3 isoform X1

Conserved Domains (3) summary

COG1196
Location:340 → 570

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

cd15744
Location:629 → 675

FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins

pfam02759
Location:171 → 292

RUN; RUN domain
XM_036165293.1 → XP_036021186.1 protein RUFY3 isoform X6

Conserved Domains (2) summary

COG1196
Location:326 → 532

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

pfam02759
Location:171 → 292

RUN; RUN domain
XM_036165295.1 → XP_036021188.1 protein RUFY3 isoform X7

Conserved Domains (2) summary

COG1196
Location:192 → 400

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

pfam02759
Location:39 → 160

RUN; RUN domain
XM_006535116.5 → XP_006535179.1 protein RUFY3 isoform X5

See identical proteins and their annotated locations for XP_006535179.1

Conserved Domains (3) summary

TIGR02168
Location:179 → 438

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd15744
Location:497 → 543

FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins

pfam02759
Location:39 → 160

RUN; RUN domain
XM_006535112.2 → XP_006535175.1 protein RUFY3 isoform X2

See identical proteins and their annotated locations for XP_006535175.1

Conserved Domains (3) summary

TIGR02168
Location:261 → 520

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd15744
Location:579 → 625

FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins

pfam02759
Location:121 → 242

RUN; RUN domain
XM_006535111.2 → XP_006535174.1 protein RUFY3 isoform X2

See identical proteins and their annotated locations for XP_006535174.1

Conserved Domains (3) summary

TIGR02168
Location:261 → 520

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd15744
Location:579 → 625

FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins

pfam02759
Location:121 → 242

RUN; RUN domain
XM_017320983.3 → XP_017176472.1 protein RUFY3 isoform X3

Conserved Domains (3) summary

TIGR02168
Location:243 → 502

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd15744
Location:561 → 607

FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins

pfam02759
Location:103 → 224

RUN; RUN domain
XM_006535114.4 → XP_006535177.1 protein RUFY3 isoform X4

Conserved Domains (3) summary

TIGR02168
Location:213 → 472

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd15744
Location:531 → 577

FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins

pfam02759
Location:73 → 194

RUN; RUN domain