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Aliases for NIF3L1 Gene

Aliases for NIF3L1 Gene

  • NGG1 Interacting Factor 3 Like 1 2 3 5
  • Amyotrophic Lateral Sclerosis 2 Chromosomal Region Candidate Gene 1 Protein 3 4
  • NIF3 (Ngg1 Interacting Factor 3, S.Pombe Homolog)-Like 1 2 3
  • NIF3 NGG1 Interacting Factor 3-Like 1 2 3
  • ALS2CR1 3 4
  • Amyotrophic Lateral Sclerosis 2 (Juvenile) Chromosome Region, Candidate 1 3
  • NIF3 NGG1 Interacting Factor 3-Like 1 (S. Cerevisiae) 2
  • NIF3 NGG1 Interacting Factor 3-Like 1 (S. Pombe) 2
  • Putative GTP Cyclohydrolase 1 Type 2 NIF3L1 3
  • GTP Cyclohydrolase I 3
  • NIF3-Like Protein 1 3
  • CALS-7 3
  • MDS015 3

External Ids for NIF3L1 Gene

Previous HGNC Symbols for NIF3L1 Gene

  • ALS2CR1

Previous GeneCards Identifiers for NIF3L1 Gene

  • GC02P199971
  • GC02P200478
  • GC02P201718
  • GC02P201956
  • GC02P201579
  • GC02P201462
  • GC02P193605

Summaries for NIF3L1 Gene

GeneCards Summary for NIF3L1 Gene

NIF3L1 (NGG1 Interacting Factor 3 Like 1) is a Protein Coding gene. Diseases associated with NIF3L1 include Williams-Beuren Syndrome and Juvenile Amyotrophic Lateral Sclerosis. Gene Ontology (GO) annotations related to this gene include identical protein binding and hydrolase activity.

UniProtKB/Swiss-Prot for NIF3L1 Gene

  • May function as a transcriptional corepressor through its interaction with COPS2, negatively regulating the expression of genes involved in neuronal differentiation.

Gene Wiki entry for NIF3L1 Gene

Additional gene information for NIF3L1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NIF3L1 Gene

Genomics for NIF3L1 Gene

GeneHancer (GH) Regulatory Elements for NIF3L1 Gene

Promoters and enhancers for NIF3L1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J200887 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 -0.1 -139 3.6 FEZF1 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 ZNF610 GLIS1 PPIL3 CLK1 NIF3L1 ORC2 TYW5 LOC100420110 RNU6-762P CASP10 RNU6-312P
GH02J200859 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.8 -26.6 -26588 6 HDGF PKNOX1 CLOCK SMAD1 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 CLK1 ENSG00000252759 GC02M200864 PPIL3 ORC2 LOC100420110 TYW5 NIF3L1 BZW1 LOC101927795
GH02J201093 Enhancer 0.6 Ensembl 11.5 +204.7 204650 0.8 SP1 JUND RXRA EGR1 REST HNF4A GABPA YY1 RNU6-312P PPIL3 CFLAR CFLAR-AS1 NIF3L1 LOC105373835 ORC2 ENSG00000273975 RNU6-1206P
GH02J201089 Enhancer 0.5 ENCODE 11.5 +200.6 200571 0.1 SP1 JUND TAF1 RXRA HNF4A REST YY1 RNU6-312P CFLAR CFLAR-AS1 NIF3L1 PPIL3 LOC105373835 ORC2 ENSG00000273975 RNU6-1206P
GH02J200962 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 1.7 +74.5 74479 3 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ORC2 LOC105373835 PPIL3 CDK15 LOC100420110 KCTD18 SGO2 CLK1 CASP8 FAM126B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NIF3L1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NIF3L1 gene promoter:
  • SRY
  • PPAR-gamma1
  • PPAR-gamma2
  • AML1a

Genomic Locations for NIF3L1 Gene

Genomic Locations for NIF3L1 Gene
14,606 bases
Plus strand
14,606 bases
Plus strand

Genomic View for NIF3L1 Gene

Genes around NIF3L1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NIF3L1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NIF3L1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NIF3L1 Gene

Proteins for NIF3L1 Gene

  • Protein details for NIF3L1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    NIF3-like protein 1
    Protein Accession:
    Secondary Accessions:
    • Q53TX4
    • Q6X735
    • Q9H2D2
    • Q9HC18

    Protein attributes for NIF3L1 Gene

    377 amino acids
    Molecular mass:
    41968 Da
    Quaternary structure:
    • Homodimer (PubMed:12951069). Interacts with COPS2 (By similarity). Interacts with THOC7 (PubMed:12951069).
    • Sequence=AAG14952.1; Type=Frameshift; Positions=104, 109; Evidence={ECO:0000305};

    Alternative splice isoforms for NIF3L1 Gene


neXtProt entry for NIF3L1 Gene

Post-translational modifications for NIF3L1 Gene

  • Ubiquitination at Lys242, isoforms=2, 3234, and Lys216
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NIF3L1 Gene

Domains & Families for NIF3L1 Gene

Gene Families for NIF3L1 Gene

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

Suggested Antigen Peptide Sequences for NIF3L1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the GTP cyclohydrolase I type 2/NIF3 family.
  • Belongs to the GTP cyclohydrolase I type 2/NIF3 family.
genes like me logo Genes that share domains with NIF3L1: view

Function for NIF3L1 Gene

Molecular function for NIF3L1 Gene

UniProtKB/Swiss-Prot Function:
May function as a transcriptional corepressor through its interaction with COPS2, negatively regulating the expression of genes involved in neuronal differentiation.

Gene Ontology (GO) - Molecular Function for NIF3L1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12951069
GO:0008134 transcription factor binding IPI 15163635
GO:0042802 identical protein binding IPI 12951069
genes like me logo Genes that share ontologies with NIF3L1: view
genes like me logo Genes that share phenotypes with NIF3L1: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NIF3L1 Gene

Localization for NIF3L1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NIF3L1 Gene

Cytoplasm. Nucleus. Note=Interaction with COPS2 may regulate localization to the nucleus. {ECO:0000250 UniProtKB:Q9EQ80}.

Subcellular locations from

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 NIF3L1 gene
Compartment Confidence
nucleus 5
mitochondrion 4
peroxisome 2
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NIF3L1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,ISS --
GO:0005737 cytoplasm IDA,IEA 12951069
GO:0005739 mitochondrion IBA --
genes like me logo Genes that share ontologies with NIF3L1: view

Pathways & Interactions for NIF3L1 Gene

SuperPathways for NIF3L1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for NIF3L1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030182 neuron differentiation ISS --
GO:0045893 positive regulation of transcription, DNA-templated IDA 15163635
GO:1903507 negative regulation of nucleic acid-templated transcription ISS --
genes like me logo Genes that share ontologies with NIF3L1: view

No data available for Pathways by source and SIGNOR curated interactions for NIF3L1 Gene

Drugs & Compounds for NIF3L1 Gene

No Compound Related Data Available

Transcripts for NIF3L1 Gene

Unigene Clusters for NIF3L1 Gene

NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NIF3L1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9
SP1: - -
SP4: -
SP5: - - - -
SP6: -
SP7: -

Relevant External Links for NIF3L1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NIF3L1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NIF3L1 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NIF3L1 Gene

Protein tissue co-expression partners for NIF3L1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NIF3L1 Gene:


SOURCE GeneReport for Unigene cluster for NIF3L1 Gene:


Evidence on tissue expression from TISSUES for NIF3L1 Gene

  • Nervous system(4.6)
  • Liver(4.2)
  • Skin(4.2)
genes like me logo Genes that share expression patterns with NIF3L1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NIF3L1 Gene

Orthologs for NIF3L1 Gene

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

Orthologs for NIF3L1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NIF3L1 34 33
  • 99.47 (n)
(Canis familiaris)
Mammalia NIF3L1 34 33
  • 88.77 (n)
(Bos Taurus)
Mammalia NIF3L1 34 33
  • 88.51 (n)
(Rattus norvegicus)
Mammalia Nif3l1 33
  • 85.83 (n)
(Mus musculus)
Mammalia Nif3l1 16 34 33
  • 85.73 (n)
(Monodelphis domestica)
Mammalia NIF3L1 34
  • 69 (a)
(Ornithorhynchus anatinus)
Mammalia NIF3L1 34
  • 62 (a)
(Gallus gallus)
Aves NIF3L1 34 33
  • 71 (n)
(Anolis carolinensis)
Reptilia NIF3L1 34
  • 66 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101733905 33
  • 60.8 (n)
Str.4241 33
(Danio rerio)
Actinopterygii nif3l1 34 33
  • 54.94 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012228 33
  • 50.81 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4278 34 35 33
  • 48.99 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NIF3 36 34 33
  • 48.81 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR233W 33
  • 47.89 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A01518g 33
  • 46.64 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPCC126.12 33
  • 50.07 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU06108 33
  • 49.58 (n)
Species where no ortholog for NIF3L1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for NIF3L1 Gene

Gene Tree for NIF3L1 (if available)
Gene Tree for NIF3L1 (if available)
Evolutionary constrained regions (ECRs) for NIF3L1: view image

Paralogs for NIF3L1 Gene

(1) SIMAP similar genes for NIF3L1 Gene using alignment to 6 proteins:

  • C9JN42_HUMAN
  • H7C1A8_HUMAN
  • Q6X734_HUMAN Pseudogenes for NIF3L1 Gene

genes like me logo Genes that share paralogs with NIF3L1: view

No data available for Paralogs for NIF3L1 Gene

Variants for NIF3L1 Gene

Sequence variations from dbSNP and Humsavar for NIF3L1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000033092 -- 200,892,373(+) G/A coding_sequence_variant, missense_variant
rs1000160673 -- 200,899,061(+) T/C intron_variant
rs1000494812 -- 200,900,641(+) A/T intron_variant
rs1000550407 -- 200,901,099(+) C/G intron_variant
rs1000653203 -- 200,900,337(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NIF3L1 Gene

Variant ID Type Subtype PubMed ID
nsv3109 CNV deletion 18451855

Variation tolerance for NIF3L1 Gene

Residual Variation Intolerance Score: 86.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.89; 89.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NIF3L1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NIF3L1 Gene

Disorders for NIF3L1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for NIF3L1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
williams-beuren syndrome
  • wbs
juvenile amyotrophic lateral sclerosis
  • amyotrophic lateral sclerosis, juvenile
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for NIF3L1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NIF3L1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NIF3L1 Gene

Publications for NIF3L1 Gene

  1. Isolation and characterization of a novel human gene, NIF3L1, and its mouse ortholog, Nif3l1, highly conserved from bacteria to mammals. (PMID: 11124544) Tascou S … Burfeind P (Cytogenetics and cell genetics 2000) 2 3 4 22 58
  2. Cloning and characterization of three novel genes, ALS2CR1, ALS2CR2, and ALS2CR3, in the juvenile amyotrophic lateral sclerosis (ALS2) critical region at chromosome 2q33-q34: candidate genes for ALS2. (PMID: 11161814) Hadano S … Hayden MR (Genomics 2001) 2 3 4 58
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 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 status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for NIF3L1 Gene

Sources for NIF3L1 Gene

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