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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 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 6.3.2.- 4
  • Listerin 2
  • KIAA0714 4

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 Immune System and Class I MHC mediated antigen processing and presentation. 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).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LTN1 Gene

Genomics for LTN1 Gene

Regulatory Elements for LTN1 Gene

Enhancers for LTN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH21F029216 1.4 FANTOM5 Ensembl ENCODE 58.5 -227.0 -226996 7.0 PKNOX1 FEZF1 ZNF2 ZNF302 FOS DEK SP3 REST MEF2D ZNF610 LTN1 RPL12P9 ENSG00000231125 BACH1 CCT8 HSPD1P7 ENSG00000259981 LINC00307 RPL23P2 ENSG00000212479
GH21F029304 0.8 ENCODE 43.4 -313.0 -312962 2.8 PKNOX1 PTRF CHAMP1 SCRT2 ZNF202 CREB3 TFDP1 ZNF292 SMARCA4 PBX2 LTN1 ENSG00000231125 RPL12P9 CCT8 ENSG00000224649 GC21P029306 GC21P029305 GC21P029329 GC21P029330
GH21F028991 0.2 ENCODE 38.5 +0.1 139 2.6 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 CCT8 LTN1 RPL12P9 RWDD2B ENSG00000231125 RPL23P2 N6AMT1 USP16 MAP3K7CL GC21M028974
GH21F029298 1.2 ENCODE 31.9 -307.9 -307891 5.8 HDGF WRNIP1 ZFP64 ARID4B SIN3A DMAP1 FOS KLF13 ZNF263 SP3 ENSG00000231125 LTN1 RPL12P9 RPL23P2 GC21P029306 LOC105369299 GC21P029305
GH21F029017 0.5 ENCODE 30.3 -26.0 -25967 2.6 ATF1 CREB3L1 MLX ARID4B SIN3A DMAP1 ZNF48 ZNF2 YY1 SLC30A9 LTN1 RWDD2B RPL12P9 ENSG00000231125 CCT8 MAP3K7CL GC21P029012
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around LTN1 on UCSC Golden Path with GeneCards custom track

Promoters for LTN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001840189 456 2201 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1

Genomic Location for LTN1 Gene

Chromosome:
21
Start:
28,928,144 bp from pter
End:
28,992,956 bp from pter
Size:
64,813 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 Lys 638, Lys 651, Lys 717, Lys 737, Lys 992, Lys 1140, and Lys 1355
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LTN1 Gene

Domains & Families for LTN1 Gene

Gene Families for LTN1 Gene

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.
  • Contains 16 HEAT repeats.
Family:
  • Belongs to the LTN1 family.
Similarity:
  • Contains 16 HEAT repeats.
  • Contains 1 RING-type zinc finger.
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).

Enzyme Numbers (IUBMB) for LTN1 Gene

Gene Ontology (GO) - Molecular Function for LTN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21903422
GO:0008270 zinc ion binding IEA --
GO:0016874 ligase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0061630 ubiquitin protein ligase activity IEA --
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

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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
Jensen Localization Image for LTN1 Gene COMPARTMENTS Subcellular localization image for LTN1 gene
Compartment Confidence
cytosol 4
nucleus 3
mitochondrion 2

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components 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:0051865 protein autoubiquitination IEA --
genes like me logo Genes that share ontologies with LTN1: view

No data available for SIGNOR curated interactions for LTN1 Gene

Transcripts for LTN1 Gene

Unigene Clusters for LTN1 Gene

Listerin E3 ubiquitin protein ligase 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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 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, PaxDb, 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
genes like me logo Genes that share expression patterns with LTN1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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 35
  • 99.5 (n)
dog
(Canis familiaris)
Mammalia LTN1 34 35
  • 91.07 (n)
cow
(Bos Taurus)
Mammalia LTN1 34
  • 89.98 (n)
RNF160 35
  • 84 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ltn1 34
  • 84.24 (n)
mouse
(Mus musculus)
Mammalia Ltn1 34 16 35
  • 83.97 (n)
oppossum
(Monodelphis domestica)
Mammalia LTN1 35
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves LTN1 34 35
  • 71.24 (n)
lizard
(Anolis carolinensis)
Reptilia LTN1 35
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ltn1 34
  • 63.11 (n)
Str.7225 34
zebrafish
(Danio rerio)
Actinopterygii si:dkey-175g6.5 34
  • 56.71 (n)
LTN1 35
  • 53 (a)
OneToOne
Dr.13250 34
fruit fly
(Drosophila melanogaster)
Insecta l(3)76BDr 35
  • 26 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y54E10A.11 35
  • 22 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RKR1 35 37
  • 19 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 27 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.543 34
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)

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 Sequence Context AA Info Type
rs1028992 -- 28,975,861(+) TCAAG(A/G)AAGAT intron-variant
rs10608923 -- 28,931,067(+) TGTAG(-/GT)GTGTG intron-variant
rs1061231 -- 28,929,924(-) TAATA(C/T)GGCTT utr-variant-3-prime
rs11088101 -- 28,930,630(+) GAACA(A/C)TAAAA intron-variant
rs11088102 -- 28,934,434(+) TTCCC(A/G)CGGGT 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)

Relevant External Links for LTN1 Gene

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

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

Disorders for LTN1 Gene

Relevant External Links for LTN1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 R.S. (Mol. Cell 2015) 3 4 64
  2. Role of a ribosome-associated E3 ubiquitin ligase in protein quality control. (PMID: 20835226) Bengtson M.H. … Joazeiro C.A. (Nature 2010) 2 3 64
  3. A mouse forward genetics screen identifies LISTERIN as an E3 ubiquitin ligase involved in neurodegeneration. (PMID: 19196968) Chu J. … Kay S.A. (Proc. Natl. Acad. Sci. U.S.A. 2009) 2 3 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The DNA sequence of human chromosome 21. (PMID: 10830953) Hattori M. … Yaspo M.-L. (Nature 2000) 3 4 64

Products for LTN1 Gene

Sources for LTN1 Gene

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