RUFY3 RUN and FYVE domain containing 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RUFY3provided by HGNC
Official Full Name: RUN and FYVE domain containing 3provided by HGNC
Primary source: HGNC:HGNC:30285
See related: Ensembl:ENSG00000018189 MIM:611194; AllianceGenome:HGNC:30285
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: RIPX; SINGAR1; ZFYVE30
Summary: This gene encodes a RPIP8, UNC-14, and NESCA domain-containing protein that is required for maintenance of neuronal polarity. In addition, it has been implicated in mediation of gastric cancer cell migration and invasion via interaction with P21-activated kinase-1, which promotes its expression. The encoded protein localizes to F-actin-enriched invadopodia to induce formation of protrusions, thereby facilitating cell migration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]
Expression: Ubiquitous expression in brain (RPKM 27.2), testis (RPKM 10.8) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q13.3

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (70703767..70808619)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (74046233..74151087)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (71570456..71674336)

Chromosome 4 - NC_000004.12 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

circSORBS1 inhibits lung cancer progression by sponging miR-6779-5p and directly binding RUFY3 mRNA.
Title: circSORBS1 inhibits lung cancer progression by sponging miR-6779-5p and directly binding RUFY3 mRNA.
HPIP and RUFY3 are noncanonical guanine nucleotide exchange factors of Rab5 to regulate endocytosis-coupled focal adhesion turnover.
Title: HPIP and RUFY3 are noncanonical guanine nucleotide exchange factors of Rab5 to regulate endocytosis-coupled focal adhesion turnover.
Low RUFY3 expression level is associated with lymph node metastasis in older women with invasive breast cancer.
Title: Low RUFY3 expression level is associated with lymph node metastasis in older women with invasive breast cancer.
RUFY3 promotes the progression of hepatocellular carcinoma through activating NF-kappaB-mediated epithelial-mesenchymal transition.
Title: RUFY3 promotes the progression of hepatocellular carcinoma through activating NF-κB-mediated epithelial-mesenchymal transition.
Crystal structure of the FYCO1 RUN domain suggests possible interfaces with small GTPases.
Title: Crystal structure of the FYCO1 RUN domain suggests possible interfaces with small GTPases.
HOXD9 directly associated with the RUFY3 promoter to increase the transcriptional activity of RUFY3 in gastric cancer.
Title: HOXD9 promotes the growth, invasion and metastasis of gastric cancer cells by transcriptional activation of RUFY3.
our results uncovered a novel, unexpected regulatory function of RUFY3. We identified FOXK1 as a new RUFY3-binding protein. This study shed light on the critical role of RUFY3 in inducing EMT and in the migration and invasion phenotypes caused by abnormal FOXK1 expression.
Title: RUFY3 interaction with FOXK1 promotes invasion and metastasis in colorectal cancer.
these findings provide important evidence that PAK1 can positively regulate RUFY3 expression, which contribute to the metastatic potential of gastric cancer cells
Title: PAK1 regulates RUFY3-mediated gastric cancer cell migration and invasion.
Rab5(Q79L) interacts with the carboxyl terminus of RUFY3
Title: Rab5(Q79L) interacts with the carboxyl terminus of RUFY3.

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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

SHGC-112396 (e-PCR)
- UniSTS:183840

RH103769 (e-PCR)
- UniSTS:98094

SHGC-34593 (e-PCR)
- UniSTS:56655

G19859 (e-PCR)
- UniSTS:32890

A002A32 (e-PCR)
- UniSTS:32891

RH12424 (e-PCR)
- UniSTS:5774

D4S2538E (e-PCR)
- UniSTS:66200

RH11635 (e-PCR)
- UniSTS:35485

RH36129 (e-PCR)
- UniSTS:92359

D4S2562E (e-PCR)
- UniSTS:70861

RH45149 (e-PCR)
- UniSTS:14821

Gene Ontology Provided by GOA

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

Process	Evidence Code	Pubs
involved_in actin filament organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of axonogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of axon extension	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of intracellular protein transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of axonogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of establishment of cell polarity	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in anchoring junction	IEA Inferred from Electronic Annotation more info
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
is_active_in dendrite	IBA Inferred from Biological aspect of Ancestor more info
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
located_in endomembrane system	IEA Inferred from Electronic Annotation more info
located_in filopodium	ISS Inferred from Sequence or Structural Similarity more info
located_in growth cone	ISS Inferred from Sequence or Structural Similarity more info
located_in lamellipodium	ISS Inferred from Sequence or Structural Similarity 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
located_in perikaryon	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: protein RUFY3

Names: rap2 interacting protein x; single axon-regulated protein; single axon-related 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.

Genomic

NG_051554.2 RefSeqGene

Range

23199..109854

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001037442.4 → NP_001032519.1 protein RUFY3 isoform 1

See identical proteins and their annotated locations for NP_001032519.1

Status: REVIEWED

Description

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

Source sequence(s)

AA435606, AC009570, AC021989, AK302637, BC053837, DA248021, DC299541

Consensus CDS

CCDS34001.1

UniProtKB/Swiss-Prot

Q7L099

Related

ENSP00000370394.3, ENST00000381006.8

Conserved Domains (2) summary

cd15744
Location:561 → 608

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

pfam02759
Location:103 → 226

RUN; RUN domain
NM_001130709.2 → NP_001124181.1 protein RUFY3 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) has multiple differences in the 5' and 3' coding regions and the 5' and 3' UTRs, compared to variant 1. The encoded protein (isoform 3) has a distinct N-terminus and a shorter C-terminus, compared to isoform 1.

Source sequence(s)

AC009570, AF112221, AK000911, BM920380, DA015234, DB482497, DB483639

Consensus CDS

CCDS47068.1

UniProtKB/Swiss-Prot

Q7L099

Related

ENSP00000399771.2, ENST00000417478.6

Conserved Domains (5) summary

pfam01442
Location:334 → 506

Apolipoprotein; Apolipoprotein A1/A4/E domain

pfam02759
Location:163 → 286

RUN; RUN domain

pfam05038
Location:21 → 64

Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit

pfam10212
Location:333 → 382

TTKRSYEDQ; Predicted coiled-coil domain-containing protein

cl23720
Location:400 → 506

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
NM_001291993.2 → NP_001278922.1 protein RUFY3 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) has an alternate 5' exon structure and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 4, which is shorter and has a distinct N-terminus, compared to isoform 1.

Source sequence(s)

AA435606, AC009570, AC021989, AK302637, BC053837, DA285699, DC299541

Consensus CDS

CCDS75138.1

UniProtKB/Swiss-Prot

Q7L099

Related

ENSP00000425400.1, ENST00000502653.5

Conserved Domains (2) summary

cd15744
Location:508 → 555

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

pfam02759
Location:50 → 173

RUN; RUN domain
NM_001291994.2 → NP_001278923.1 protein RUFY3 isoform 5

See identical proteins and their annotated locations for NP_001278923.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 5' coding region and has an alternate 3' exon structure, compared to variant 1. It encodes isoform 5, which is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AC009570

UniProtKB/TrEMBL

B4DKC2

Conserved Domains (2) summary

COG1196
Location:276 → 482

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

pfam02759
Location:121 → 242

RUN; RUN domain
NM_001345840.2 → NP_001332769.1 protein RUFY3 isoform 6

Status: REVIEWED

Description

Transcript Variant: This variant (6) represents use of an alternate promoter, uses an alternate start codon, and has an alternate 3' exon structure compared to variant 1. It encodes isoform 6, which is shorter than and has distinct N- and C-termini compared to isoform 1.

Source sequence(s)

AC009570

UniProtKB/TrEMBL

B4DG59

Conserved Domains (2) summary

pfam02759
Location:50 → 171

RUN; RUN domain

cl25732
Location:203 → 411

SMC_N; RecF/RecN/SMC N terminal domain
NM_014961.5 → NP_055776.1 protein RUFY3 isoform 2

See identical proteins and their annotated locations for NP_055776.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has multiple differences in the 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AC009570

Consensus CDS

CCDS3547.1

UniProtKB/Swiss-Prot

B3KM25, B4DYW7, D9N163, O94948, Q7L099, Q9UI00

UniProtKB/TrEMBL

B4DG59

Related

ENSP00000226328.4, ENST00000226328.8

Conserved Domains (2) summary

COG1196
Location:258 → 464

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

pfam02759
Location:103 → 224

RUN; RUN domain

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

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

70703767..70808619

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011531750.3 → XP_011530052.1 protein RUFY3 isoform X1

Conserved Domains (5) summary

cd15744
Location:621 → 668

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

pfam01442
Location:334 → 507

Apolipoprotein; Apolipoprotein A1/A4/E domain

pfam02759
Location:163 → 286

RUN; RUN domain

pfam05038
Location:21 → 64

Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit

pfam15960
Location:402 → 558

DUF4763; Domain of unknown function (DUF4763)
XM_005265656.4 → XP_005265713.1 protein RUFY3 isoform X3

Conserved Domains (2) summary

cd15744
Location:579 → 626

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

pfam02759
Location:121 → 244

RUN; RUN domain
XM_047449825.1 → XP_047305781.1 protein RUFY3 isoform X1
XM_011531751.4 → XP_011530053.1 protein RUFY3 isoform X2

Conserved Domains (5) summary

cd15744
Location:611 → 645

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

pfam01442
Location:334 → 507

Apolipoprotein; Apolipoprotein A1/A4/E domain

pfam02759
Location:163 → 286

RUN; RUN domain

pfam05038
Location:21 → 64

Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit

pfam15960
Location:402 → 558

DUF4763; Domain of unknown function (DUF4763)
XM_047449827.1 → XP_047305783.1 protein RUFY3 isoform X5
XM_011531756.4 → XP_011530058.1 protein RUFY3 isoform X9

Conserved Domains (5) summary

pfam01442
Location:334 → 507

Apolipoprotein; Apolipoprotein A1/A4/E domain

pfam02759
Location:163 → 286

RUN; RUN domain

pfam05038
Location:21 → 64

Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit

pfam10212
Location:333 → 382

TTKRSYEDQ; Predicted coiled-coil domain-containing protein

cl23720
Location:400 → 506

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
XM_047449828.1 → XP_047305784.1 protein RUFY3 isoform X6
XM_011531755.4 → XP_011530057.1 protein RUFY3 isoform X8

Conserved Domains (5) summary

pfam01442
Location:334 → 506

Apolipoprotein; Apolipoprotein A1/A4/E domain

pfam02759
Location:163 → 286

RUN; RUN domain

pfam05038
Location:21 → 64

Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit

pfam10212
Location:333 → 382

TTKRSYEDQ; Predicted coiled-coil domain-containing protein

cl23720
Location:400 → 528

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
XM_047449826.1 → XP_047305782.1 protein RUFY3 isoform X4
XM_047449829.1 → XP_047305785.1 protein RUFY3 isoform X10
XM_047449830.1 → XP_047305786.1 protein RUFY3 isoform X11
XM_005265658.3 → XP_005265715.1 protein RUFY3 isoform X7

Conserved Domains (2) summary

cd15744
Location:497 → 544

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

pfam02759
Location:39 → 162

RUN; RUN domain