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Aliases for RNFT1 Gene

Aliases for RNFT1 Gene

  • Ring Finger Protein, Transmembrane 1 2 3 5
  • RING Finger And Transmembrane Domain-Containing Protein 1 3 4
  • E3 Ubiquitin-Protein Ligase RNFT1 3
  • Protein PTD016 4
  • EC 2.3.2.27 4
  • PTD016 3

External Ids for RNFT1 Gene

Previous GeneCards Identifiers for RNFT1 Gene

  • GC17M055387
  • GC17M058029
  • GC17M053402

Summaries for RNFT1 Gene

GeneCards Summary for RNFT1 Gene

RNFT1 (Ring Finger Protein, Transmembrane 1) is a Protein Coding gene. Diseases associated with RNFT1 include Spermatogenic Failure, X-Linked, 1. An important paralog of this gene is RNFT2.

UniProtKB/Swiss-Prot for RNFT1 Gene

  • E3 ubiquitin-protein ligase that acts in the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway, which targets misfolded proteins that accumulate in the endoplasmic reticulum (ER) for ubiquitination and subsequent proteasome-mediated degradation. Protects cells from ER stress-induced apoptosis.

Additional gene information for RNFT1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RNFT1 Gene

Genomics for RNFT1 Gene

GeneHancer (GH) Regulatory Elements for RNFT1 Gene

Promoters and enhancers for RNFT1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17I059963 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 561.1 +0.3 261 2.1 PKNOX1 ARNT ARID4B SIN3A DMAP1 YY1 POLR2B E2F8 ZNF207 SP5 RNFT1-DT RNFT1 SMG8 PPM1D TUBD1 HEATR6 NDUFB8P2 ENSG00000274378 DHX40 ENSG00000267318
GH17I059151 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE 23.8 +808.5 808471 9.6 CLOCK ZFP64 YBX1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 SP3 NFYC GC17M059154 PRR11 SKA2 MKS1 NDUFB8P2 TUBD1 TRIM37 RPS6KB1 SMG8 RNFT1
GH17I059209 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 23.8 +754.5 754473 2.2 MLX ZFP64 YBX1 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 SMG8 TUBD1 RPS6KB1 MKS1 HEATR6 TRIM37 RNFT1 NDUFB8P2 SKA2 DHX40
GH17I059616 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 16.8 +345.1 345086 6.8 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 CLTC ENSG00000273702 TUBD1 RPS6KB1 HEATR6 SKA2 PPM1D DHX40 RNFT1 NDUFB8P2
GH17I059327 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 15.2 +634.2 634202 6 PKNOX1 CLOCK FOXA2 ARID4B SIN3A DMAP1 ZBTB7B YY1 ZNF207 ZNF143 YPEL2 RNFT1 NDUFB8P2 RPS6KB1 TUBD1 HEATR6 TEX14 SKA2 SNRPGP17
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RNFT1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RNFT1 gene promoter:

Genomic Locations for RNFT1 Gene

Genomic Locations for RNFT1 Gene
chr17:59,952,240-59,964,761
(GRCh38/hg38)
Size:
12,522 bases
Orientation:
Minus strand
chr17:58,029,601-58,042,122
(GRCh37/hg19)

Genomic View for RNFT1 Gene

Genes around RNFT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNFT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNFT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNFT1 Gene

Proteins for RNFT1 Gene

  • Protein details for RNFT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5M7Z0-RNFT1_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase RNFT1
    Protein Accession:
    Q5M7Z0
    Secondary Accessions:
    • Q8N7D0
    • Q96IZ9
    • Q9Y686

    Protein attributes for RNFT1 Gene

    Size:
    435 amino acids
    Molecular mass:
    49710 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAD43009.1; Type=Frameshift; Positions=150, 167; Evidence={ECO:0000305}; Sequence=BAC05364.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for RNFT1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RNFT1 Gene

Post-translational modifications for RNFT1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RNFT1 Gene

No data available for DME Specific Peptides for RNFT1 Gene

Domains & Families for RNFT1 Gene

Gene Families for RNFT1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for RNFT1 Gene

Suggested Antigen Peptide Sequences for RNFT1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RNFT1: view

No data available for UniProtKB/Swiss-Prot for RNFT1 Gene

Function for RNFT1 Gene

Molecular function for RNFT1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.
UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase that acts in the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway, which targets misfolded proteins that accumulate in the endoplasmic reticulum (ER) for ubiquitination and subsequent proteasome-mediated degradation. Protects cells from ER stress-induced apoptosis.
UniProtKB/Swiss-Prot Induction:
Up-regulated by endoplasmic reticulum (ER) stress triggered by thapsigargin or tunicamycin.

Enzyme Numbers (IUBMB) for RNFT1 Gene

Phenotypes From GWAS Catalog for RNFT1 Gene

Gene Ontology (GO) - Molecular Function for RNFT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RNFT1: view
genes like me logo Genes that share phenotypes with RNFT1: view

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RNFT1 Gene

Localization for RNFT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RNFT1 Gene

Endoplasmic reticulum membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RNFT1 gene
Compartment Confidence
nucleus 3
endoplasmic reticulum 3
plasma membrane 2
peroxisome 2
cytosol 2
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RNFT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with RNFT1: view

Pathways & Interactions for RNFT1 Gene

SuperPathways for RNFT1 Gene

No Data Available

UniProtKB/Swiss-Prot Q5M7Z0-RNFT1_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for RNFT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016567 protein ubiquitination IEA --
genes like me logo Genes that share ontologies with RNFT1: view

No data available for Pathways by source and SIGNOR curated interactions for RNFT1 Gene

Drugs & Compounds for RNFT1 Gene

No Compound Related Data Available

Transcripts for RNFT1 Gene

Unigene Clusters for RNFT1 Gene

Ring finger protein, transmembrane 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RNFT1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17
SP1:
SP2:
SP3: -
SP4:
SP5:
SP6: - - -

Relevant External Links for RNFT1 Gene

GeneLoc Exon Structure for
RNFT1
ECgene alternative splicing isoforms for
RNFT1

Expression for RNFT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNFT1 Gene

mRNA differential expression in normal tissues according to GTEx for RNFT1 Gene

This gene is overexpressed in Testis (x5.0).

Protein differential expression in normal tissues from HIPED for RNFT1 Gene

This gene is overexpressed in Plasma (58.0) and Testis (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RNFT1 Gene



Protein tissue co-expression partners for RNFT1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RNFT1 Gene:

RNFT1

SOURCE GeneReport for Unigene cluster for RNFT1 Gene:

Hs.531701

mRNA Expression by UniProt/SwissProt for RNFT1 Gene:

Q5M7Z0-RNFT1_HUMAN
Tissue specificity: Expressed at highest levels in testis, lower levels in heart, liver, lung, and kidney (PubMed:17074343). Not detected in brain, ovary, and uterus (PubMed:17074343). Down-regulated in testis from patients with maturation arrest (MA) or Sertoli cell-only syndrome (SCOS) (PubMed:17074343). Ubiquitously expressed with high expression in testis (PubMed:27485036).

Evidence on tissue expression from TISSUES for RNFT1 Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with RNFT1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for RNFT1 Gene

Orthologs for RNFT1 Gene

This gene was present in the common ancestor of animals.

Orthologs for RNFT1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RNFT1 33 34
  • 99.77 (n)
dog
(Canis familiaris)
Mammalia RNFT1 33 34
  • 91.94 (n)
mouse
(Mus musculus)
Mammalia Rnft1 33 16 34
  • 87.26 (n)
cow
(Bos Taurus)
Mammalia RNFT1 34
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rnft1 33
  • 86.4 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RNFT1 34
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RNFT1 34
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves RNFT1 33 34
  • 72.5 (n)
lizard
(Anolis carolinensis)
Reptilia RNFT1 34
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rnft1 33
  • 67.01 (n)
Str.9619 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.34003 33
zebrafish
(Danio rerio)
Actinopterygii rnft1 33 34
  • 58.86 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG13605 34
  • 13 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ZC13.1 34
  • 17 (a)
OneToMany
Species where no ortholog for RNFT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RNFT1 Gene

ENSEMBL:
Gene Tree for RNFT1 (if available)
TreeFam:
Gene Tree for RNFT1 (if available)

Paralogs for RNFT1 Gene

Paralogs for RNFT1 Gene

(2) SIMAP similar genes for RNFT1 Gene using alignment to 5 proteins:

Pseudogenes.org Pseudogenes for RNFT1 Gene

genes like me logo Genes that share paralogs with RNFT1: view

Variants for RNFT1 Gene

Sequence variations from dbSNP and Humsavar for RNFT1 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000522282 -- 59,957,023(-) C/T intron_variant
rs1000553592 -- 59,960,488(-) G/A intron_variant
rs1000834952 -- 59,966,268(-) C/T upstream_transcript_variant
rs1000888696 -- 59,965,980(-) C/T upstream_transcript_variant
rs1001327092 -- 59,959,227(-) C/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RNFT1 Gene

Variant ID Type Subtype PubMed ID
esv2758700 CNV gain+loss 17122850
nsv428348 CNV gain 18775914
nsv471544 CNV gain 19718026
nsv471702 CNV gain 15918152
nsv833502 CNV gain 17160897
nsv9577 CNV gain 18304495

Variation tolerance for RNFT1 Gene

Residual Variation Intolerance Score: 83% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.88; 35.19% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RNFT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNFT1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RNFT1 Gene

Disorders for RNFT1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RNFT1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
spermatogenic failure, x-linked, 1
  • spgfx1
- elite association - COSMIC cancer census association via MalaCards
Search RNFT1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RNFT1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with RNFT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RNFT1 Gene

Publications for RNFT1 Gene

  1. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. Genome-wide identification and gene expression profiling of ubiquitin ligases for endoplasmic reticulum protein degradation. (PMID: 27485036) Kaneko M … Nomura Y (Scientific reports 2016) 4 58
  5. A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. (PMID: 24104479) Vizeacoumar FJ … Moffat J (Molecular systems biology 2013) 3 58

Products for RNFT1 Gene

Sources for RNFT1 Gene

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