LTN1 Gene (Protein Coding)

Listerin E3 Ubiquitin Protein Ligase 1

GC21M028928
GIFtS:
34
Like most RING finger proteins, LTN1 functions as an E3 ubiquitin ligase (Chu et al., 2009 [PubMed 19196968]).[supplied by OMIM, Nov 2010] See more...

Aliases for LTN1 Gene

Aliases for LTN1 Gene

  • Listerin E3 Ubiquitin Protein Ligase 1 2 3 5
  • Zinc Finger Protein 294 2 3 4
  • RING-Type E3 Ubiquitin Transferase Listerin 3 4
  • E3 Ubiquitin-Protein Ligase Listerin 3 4
  • Ring Finger Protein 160 2 3
  • C21orf10 3 4
  • C21orf98 3 4
  • KIAA0714 2 4
  • RNF160 3 4
  • ZNF294 3 4
  • Chromosome 21 Open Reading Frame 98 2
  • RING Finger Protein 160 4
  • EC 2.3.2.27 4
  • Listerin 2
  • FLJ11053 2
  • LISTERIN 2
  • LTN1 5

External Ids for LTN1 Gene

Previous HGNC Symbols for LTN1 Gene

  • C21orf98
  • C21orf10
  • ZNF294
  • RNF160

Previous GeneCards Identifiers for LTN1 Gene

  • GC21M015705
  • GC21M030302

Summaries for LTN1 Gene

Entrez Gene Summary for LTN1 Gene

  • Like most RING finger proteins, LTN1 functions as an E3 ubiquitin ligase (Chu et al., 2009 [PubMed 19196968]).[supplied by OMIM, Nov 2010]

GeneCards Summary for LTN1 Gene

LTN1 (Listerin E3 Ubiquitin Protein Ligase 1) is a Protein Coding gene. Among its related pathways are Innate Immune System and Class I MHC mediated antigen processing and presentation. Gene Ontology (GO) annotations related to this gene include binding and ubiquitin-protein transferase activity.

UniProtKB/Swiss-Prot Summary for LTN1 Gene

  • E3 ubiquitin-protein ligase component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation (PubMed:23685075, PubMed:25132172, PubMed:25578875). Ubiquitination leads to VCP/p97 recruitment for extraction and degradation of the incomplete translation product (By similarity).

Additional gene information for LTN1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LTN1 Gene

Genomics for LTN1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for LTN1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LTN1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LTN1

Genomic Locations for LTN1 Gene

Genomic Locations for LTN1 Gene
chr21:28,928,144-28,992,988
(GRCh38/hg38)
Size:
64,845 bases
Orientation:
Minus strand
chr21:30,300,466-30,365,277
(GRCh37/hg19)
Size:
64,812 bases
Orientation:
Minus strand

Genomic View for LTN1 Gene

Genes around LTN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LTN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LTN1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for LTN1 Gene

Proteins for LTN1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for LTN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O94822-LTN1_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase listerin
    Protein Accession:
    O94822
    Secondary Accessions:
    • A6NL41
    • A7E2D0
    • B2RTS0
    • C9J7U3
    • J3KPL4
    • Q05C47
    • Q9H8M4
    • Q9NUY5
    • Q9P0E9

    Protein attributes for LTN1 Gene

    Size:
    1766 amino acids
    Molecular mass:
    200552 Da
    Quaternary structure:
    • Component of the ribosome quality control complex (RQC), composed of at least the E3 ubiquitin ligase LTN1 and NEMF (PubMed:25578875). The complex probably also contains TCF25 as well as VCP/p97 and its ubiquitin-binding cofactors (By similarity). RQC forms a stable complex with 60S ribosomal subunits (PubMed:25578875).
    SequenceCaution:
    • Sequence=AAF28910.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAH29371.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA34434.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=BAA91976.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=CAB90430.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LTN1 Gene

    Alternative splice isoforms for LTN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LTN1 Gene

Protein Expression for LTN1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for LTN1 Gene

  • Autoubiquitinated.
  • Ubiquitination at Lys638, Lys651, Lys717, Lys737, Lys992, Lys1140, and Lys1355
  • Modification sites at PhosphoSitePlus

Other Protein References for LTN1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LTN1 Gene

Domains & Families for LTN1 Gene

Gene Families for LTN1 Gene

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

Protein Domains for LTN1 Gene

InterPro:
Blocks:
  • Zn-finger, RING
ProtoNet:

Suggested Antigen Peptide Sequences for LTN1 Gene

GenScript: Design optimal peptide antigens:
  • Zinc finger protein 294 (LTN1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O94822

UniProtKB/Swiss-Prot:

LTN1_HUMAN :
  • Belongs to the LTN1 family.
Family:
  • Belongs to the LTN1 family.
genes like me logo Genes that share domains with LTN1: view

Function for LTN1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for LTN1 Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation (PubMed:23685075, PubMed:25132172, PubMed:25578875). Ubiquitination leads to VCP/p97 recruitment for extraction and degradation of the incomplete translation product (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=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.; EC=2.3.2.27;.

Enzyme Numbers (IUBMB) for LTN1 Gene

Phenotypes From GWAS Catalog for LTN1 Gene

Gene Ontology (GO) - Molecular Function for LTN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity IEA --
GO:0005515 protein binding IPI 21903422
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
GO:0043023 ribosomal large subunit binding IBA 21873635
genes like me logo Genes that share ontologies with LTN1: view
genes like me logo Genes that share phenotypes with LTN1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LTN1

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LTN1 Gene

Localization for LTN1 Gene

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 LTN1 gene
Compartment Confidence
cytosol 5
nucleus 3
mitochondrion 2
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LTN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol IBA 21873635
GO:1990112 RQC complex IBA 21873635
genes like me logo Genes that share ontologies with LTN1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for LTN1 Gene

Pathways & Interactions for LTN1 Gene

genes like me logo Genes that share pathways with LTN1: view

UniProtKB/Swiss-Prot O94822-LTN1_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for LTN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016567 protein ubiquitination IEA --
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process IBA 21873635
GO:0051865 protein autoubiquitination IEA --
GO:0072344 rescue of stalled ribosome IBA 21873635
GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process IBA 21873635
genes like me logo Genes that share ontologies with LTN1: view

No data available for SIGNOR curated interactions for LTN1 Gene

Drugs & Compounds for LTN1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for LTN1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for LTN1 Gene

2 REFSEQ mRNAs :
23 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LTN1

Alternative Splicing Database (ASD) splice patterns (SP) for LTN1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15a · 15b ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20 ^
SP1: - - - -
SP2:
SP3:
SP4:
SP5:

ExUns: 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32a · 32b ^ 33
SP1: -
SP2:
SP3:
SP4:
SP5:

Relevant External Links for LTN1 Gene

GeneLoc Exon Structure for
LTN1

Expression for LTN1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LTN1 Gene

mRNA expression in normal human tissues for LTN1 Gene
mRNA expression by GTEx for LTN1 GenemRNA expression by BioGPS for LTN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LTN1 Gene

This gene is overexpressed in Bone (27.4) and Brain (11.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LTN1 Gene



Protein tissue co-expression partners for LTN1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LTN1

SOURCE GeneReport for Unigene cluster for LTN1 Gene:

Hs.288773

Evidence on tissue expression from TISSUES for LTN1 Gene

  • Nervous system(4.4)
  • Blood(4.3)
  • Bone marrow(4.2)
genes like me logo Genes that share expression patterns with LTN1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LTN1 Gene

Orthologs for LTN1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for LTN1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia LTN1 30 31
  • 99.5 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia LTN1 30 31
  • 91.07 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia LTN1 30
  • 89.98 (n)
RNF160 31
  • 84 (a)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Ltn1 30
  • 84.24 (n)
Mouse
(Mus musculus)
 Mammalia Ltn1 30 17 31
  • 83.97 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia LTN1 31
  • 71 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves LTN1 30 31
  • 71.24 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia LTN1 31
  • 66 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia ltn1 30
  • 63.11 (n)
Str.7225 30
Zebrafish
(Danio rerio)
 Actinopterygii si:dkey-175g6.5 30
  • 56.71 (n)
LTN1 31
  • 53 (a)
 OneToOne
Dr.13250 30
Fruit Fly
(Drosophila melanogaster)
 Insecta l(3)76BDr 31
  • 26 (a)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea Y54E10A.11 31
  • 22 (a)
 OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes RKR1 31 33
  • 19 (a)
 OneToOne
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 27 (a)
 OneToOne
Sea Vase
(Ciona intestinalis)
 Ascidiacea Cin.543 30
Species where no ortholog for LTN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • 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 LTN1 Gene

ENSEMBL:
Gene Tree for LTN1 (if available)
TreeFam:
Gene Tree for LTN1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LTN1: view image

Paralogs for LTN1 Gene

No data available for Paralogs for LTN1 Gene

Variants for LTN1 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LTN1 Gene

SNP ID Clinical significance and condition Chr 21 pos Variation AA Info Type
708013 Likely Benign: not provided 28,958,490(-) T/C SYNONYMOUS_VARIANT
744096 Likely Benign: not provided 28,971,391(-) C/T SYNONYMOUS_VARIANT
771781 Benign: not provided 28,966,992(-) G/A MISSENSE_VARIANT
785670 Benign: not provided 28,967,105(-) T/G MISSENSE_VARIANT
rs16983580 - p.Ala500Val

Additional dbSNP identifiers (rs#s) for LTN1 Gene

Structural Variations from Database of Genomic Variants (DGV) for LTN1 Gene

Variant ID Type Subtype PubMed ID
esv3893402 CNV gain 25118596
esv993752 CNV loss 20482838

Variation tolerance for LTN1 Gene

Residual Variation Intolerance Score: 4.82% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.18; 95.19% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LTN1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LTN1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LTN1 Gene

Disorders for LTN1 Gene

Additional Disease Information for LTN1

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform

No disorders were found for LTN1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LTN1 Gene

Publications for LTN1 Gene

  1. Structure and assembly pathway of the ribosome quality control complex. (PMID: 25578875) Shao S … Hegde RS (Molecular cell 2015) 3 4
  2. Role of a ribosome-associated E3 ubiquitin ligase in protein quality control. (PMID: 20835226) Bengtson MH … Joazeiro CA (Nature 2010) 2 3
  3. A mouse forward genetics screen identifies LISTERIN as an E3 ubiquitin ligase involved in neurodegeneration. (PMID: 19196968) Chu J … Kay SA (Proceedings of the National Academy of Sciences of the United States of America 2009) 2 3
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The DNA sequence of human chromosome 21. (PMID: 10830953) Hattori M … Chromosome 21 mapping and sequencing consortium (Nature 2000) 3 4

ExternalLinks

View latest publications for LTN1 gene in Mastermind

Products for LTN1 Gene

  • Addgene plasmids for LTN1

Sources for LTN1 Gene