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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
  • Ring Finger Protein 160 2 3
  • C21orf10 3 4
  • C21orf98 3 4
  • RNF160 3 4
  • ZNF294 3 4
  • E3 Ubiquitin-Protein Ligase Listerin 3
  • Chromosome 21 Open Reading Frame 98 2
  • RING Finger Protein 160 4
  • EC 2.3.2.27 4
  • KIAA0714 4
  • Listerin 2

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 Class I MHC mediated antigen processing and presentation and Innate Immune System. Gene Ontology (GO) annotations related to this gene include binding and ubiquitin-protein transferase activity.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for LTN1 Gene

Genomics for LTN1 Gene

GeneHancer (GH) Regulatory Elements for LTN1 Gene

Promoters and enhancers for LTN1 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
GH21J028991 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 680.9 +0.1 139 2.6 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 SP3 LTN1 LOC105372766 CCT8 RPL12P9 USP16 RWDD2B ENSG00000231125 RPL23P2 N6AMT1 MAP3K7CL
GH21J029297 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 42.9 -307.9 -307890 5.8 ZFP64 DMAP1 IRF4 YY1 SP3 ZFP41 SSRP1 GLIS1 NBN KDM1A BACH1 ENSG00000231125 RPL23P2 USP16 LTN1 RPL12P9 N6AMT1 LOC105369299 GC21P029306 GC21P029305
GH21J029216 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 51.2 -227.0 -226995 7 PKNOX1 FOXA2 FEZF1 ZNF2 YY1 ZNF213 FOS DEK SP3 ZNF662 LTN1 ENSG00000231125 RPL23P2 USP16 RPL12P9 BACH1 HSPD1P7 ENSG00000259981 LINC00307 CCT8
GH21J029075 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 31.2 -85.6 -85626 6.1 PKNOX1 SMAD1 ZNF133 SIN3A YY1 ZNF207 ZNF548 SP3 NFYC TSHZ1 MAP3K7CL GC21P029079 ENSG00000231125 LTN1 CCT8 RWDD2B RPL12P9 USP16 RPL23P2 GRIK1-AS1
GH21J029017 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 30.7 -26.0 -25967 2.6 HDGF SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 RWDD2B LTN1 ENSG00000231125 RPL12P9 CCT8 MAP3K7CL GC21P029012
- 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 UCSC Golden Path with GeneCards custom track

Genomic Locations for LTN1 Gene

Genomic Locations for LTN1 Gene
chr21:28,928,144-28,992,956
(GRCh38/hg38)
Size:
64,813 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 StructureGene Density

RefSeq DNA sequence for LTN1 Gene

Proteins for LTN1 Gene

  • 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; Positions=213, 328, 333, 342, 352, 354; 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=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAA91976.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; 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

Post-translational modifications for LTN1 Gene

  • Autoubiquitinated.
  • Ubiquitination at posLast=13551355, posLast=11401140, posLast=992992, isoforms=3737, isoforms=3717, posLast=651651, and isoforms=3638
  • Modification sites at PhosphoSitePlus

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

Suggested Antigen Peptide Sequences for LTN1 Gene

GenScript: Design optimal peptide antigens:

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

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:
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.

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:0005488 binding 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 --
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 4
nucleus 3
mitochondrion 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LTN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol IBA --
GO:0005840 COLOCALIZES_WITH ribosome IBA --
GO:1990112 RQC complex IBA --
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 --
GO:0051865 protein autoubiquitination IEA --
GO:0072344 rescue of stalled ribosome IBA --
GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process IBA --
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

No Compound Related Data Available

Transcripts for LTN1 Gene

Unigene Clusters for LTN1 Gene

Listerin E3 ubiquitin protein ligase 1:
Representative Sequences:

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
ECgene alternative splicing isoforms for
LTN1

Expression for LTN1 Gene

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

NURSA nuclear receptor signaling pathways regulating expression of LTN1 Gene:

LTN1

SOURCE GeneReport for Unigene cluster for LTN1 Gene:

Hs.288773

Evidence on tissue expression from TISSUES for LTN1 Gene

  • Blood(4.2)
  • Bone marrow(4.2)
  • Nervous system(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 34 33
  • 99.5 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LTN1 34 33
  • 91.07 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LTN1 33
  • 89.98 (n)
RNF160 34
  • 84 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ltn1 33
  • 84.24 (n)
mouse
(Mus musculus)
Mammalia Ltn1 16 34 33
  • 83.97 (n)
oppossum
(Monodelphis domestica)
Mammalia LTN1 34
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves LTN1 34 33
  • 71.24 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LTN1 34
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ltn1 33
  • 63.11 (n)
Str.7225 33
zebrafish
(Danio rerio)
Actinopterygii si:dkey-175g6.5 33
  • 56.71 (n)
LTN1 34
  • 53 (a)
OneToOne
Dr.13250 33
fruit fly
(Drosophila melanogaster)
Insecta l(3)76BDr 34
  • 26 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y54E10A.11 34
  • 22 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RKR1 36 34
  • 19 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 27 (a)
OneToOne
Cin.543 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.543 33
Species where no ortholog for LTN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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

Sequence variations from dbSNP and Humsavar for LTN1 Gene

SNP ID Clin Chr 21 pos Variation AA Info Type
rs1000136079 -- 28,965,073(-) G/A 5_prime_UTR_variant, intron_variant
rs1000171676 -- 28,968,164(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000273739 -- 28,964,830(-) C/T 5_prime_UTR_variant, intron_variant
rs1000282944 -- 28,962,505(-) G/A intron_variant
rs1000372099 -- 28,955,193(-) G/A genic_downstream_transcript_variant, intron_variant

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

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 58
  2. Role of a ribosome-associated E3 ubiquitin ligase in protein quality control. (PMID: 20835226) Bengtson MH … Joazeiro CA (Nature 2010) 2 3 58
  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 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The DNA sequence of human chromosome 21. (PMID: 10830953) Hattori M … Chromosome 21 mapping and sequencing consortium (Nature 2000) 3 4 58

Products for LTN1 Gene

Sources for LTN1 Gene

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