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    NIF3L1 NGG1 interacting factor 3 like 1 [ Homo sapiens (human) ]

    Gene ID: 60491, updated on 10-Dec-2024

    Summary

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    Official Symbol
    NIF3L1provided by HGNC
    Official Full Name
    NGG1 interacting factor 3 like 1provided by HGNC
    Primary source
    HGNC:HGNC:13390
    See related
    Ensembl:ENSG00000196290 MIM:605778; AllianceGenome:HGNC:13390
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CALS-7; MDS015; ALS2CR1
    Summary
    Enables RNA polymerase II-specific DNA-binding transcription factor binding activity and identical protein binding activity. Involved in positive regulation of DNA-templated transcription. Located in cytoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 6.5), testis (RPKM 6.0) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See NIF3L1 in Genome Data Viewer
    Location:
    2q33.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (200889327..200903932)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (201372777..201387382)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (201754050..201768655)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16965 Neighboring gene CDC like kinase 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:201753436-201754635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16968 Neighboring gene RNA, U6 small nuclear 312, pseudogene Neighboring gene peptidylprolyl isomerase like 3 Neighboring gene RNA, U6 small nuclear 762, pseudogene Neighboring gene origin recognition complex subunit 2 Neighboring gene OCT4 hESC enhancer GRCh37_chr2:201799831-201800332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16969 Neighboring gene uncharacterized LOC105373835 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:201828394-201828792 Neighboring gene hyccin PI4KA lipid kinase complex subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16970 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:201907391-201907902 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:201907903-201908415 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 35

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. The role of transcriptional corepressor Nif3l1 in early stage of neural differentiation via cooperation with Trip15/CSN2. Akiyama H, et al. J Biol Chem, 2003 Mar 21. PMID 12522100
    2. Identification and characterization of NIF3L1 BP1, a novel cytoplasmic interaction partner of the NIF3L1 protein. Tascou S, et al. Biochem Biophys Res Commun, 2003 Sep 19. PMID 12951069
    3. 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. Hadano S, et al. Genomics, 2001 Jan 15. PMID 11161814
    4. The subcellular localization of the ChoRE-binding protein, encoded by the Williams-Beuren syndrome critical region gene 14, is regulated by 14-3-3. Merla G, et al. Hum Mol Genet, 2004 Jul 15. PMID 15163635
    5. Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses. Simonis N, et al. Retrovirology, 2012 Mar 29. PMID 22458338, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    NIF3-like protein 1
    Names
    GTP cyclohydrolase I
    NIF3 (Ngg1 interacting factor 3, S.pombe homolog)-like 1
    NIF3 NGG1 interacting factor 3-like 1
    amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 1
    amyotrophic lateral sclerosis 2 chromosomal region candidate gene 1 protein
    putative GTP cyclohydrolase 1 type 2 NIF3L1
    NP_001129511.1
    NP_001135827.1
    NP_001135828.1
    NP_001356370.1
    NP_001356371.1
    NP_001356372.1
    NP_001356373.1
    NP_001356374.1
    NP_068596.2
    XP_047301327.1
    XP_047301328.1
    XP_054199248.1
    XP_054199249.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001136039.2 → NP_001129511.1  NIF3-like protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001129511.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AF283538, BM974977, BP194872
      Consensus CDS
      CCDS46485.1
      UniProtKB/Swiss-Prot
      Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
      UniProtKB/TrEMBL
      Q658J0
      Conserved Domains (1) summary
      pfam01784
      Location:33 → 354
      NIF3; NIF3 (NGG1p interacting factor 3)

    2. NM_001142355.1 → NP_001135827.1  NIF3-like protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001135827.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses a downstream in-frame translation initiation codon, compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 1. Both variants 2 and 3 encode the same isoform.
      Source sequence(s)
      AF060513, BM974977, BP194872
      Consensus CDS
      CCDS42797.1
      UniProtKB/TrEMBL
      Q658J0
      Conserved Domains (1) summary
      pfam01784
      Location:6 → 327
      NIF3; NIF3 (NGG1p interacting factor 3)

    3. NM_001142356.1 → NP_001135828.1  NIF3-like protein 1 isoform 3

      See identical proteins and their annotated locations for NP_001135828.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate exon in the 3' coding region, compared to variant 1, resulting in a frameshift. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AY251943, BM974977
      Consensus CDS
      CCDS46486.1
      UniProtKB/TrEMBL
      Q6X734
      Related
      ENSP00000387021.1, ENST00000409588.1
      Conserved Domains (1) summary
      pfam01784
      Location:33 → 196
      NIF3; NIF3 (NGG1p interacting factor 3)

    4. NM_001369441.2 → NP_001356370.1  NIF3-like protein 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC005037
      Consensus CDS
      CCDS46485.1
      UniProtKB/Swiss-Prot
      Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
      UniProtKB/TrEMBL
      Q658J0
      Related
      ENSP00000386394.1, ENST00000409020.6
      Conserved Domains (1) summary
      pfam01784
      Location:33 → 354
      NIF3; NIF3 (NGG1p interacting factor 3)

    5. NM_001369442.1 → NP_001356371.1  NIF3-like protein 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC005037
      Consensus CDS
      CCDS46485.1
      UniProtKB/Swiss-Prot
      Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
      UniProtKB/TrEMBL
      Q658J0
      Conserved Domains (1) summary
      pfam01784
      Location:33 → 354
      NIF3; NIF3 (NGG1p interacting factor 3)

    6. NM_001369443.1 → NP_001356372.1  NIF3-like protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC005037
      Consensus CDS
      CCDS42797.1
      UniProtKB/TrEMBL
      Q658J0
      Conserved Domains (1) summary
      pfam01784
      Location:6 → 327
      NIF3; NIF3 (NGG1p interacting factor 3)

    7. NM_001369444.1 → NP_001356373.1  NIF3-like protein 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC005037
      Consensus CDS
      CCDS46485.1
      UniProtKB/Swiss-Prot
      Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
      UniProtKB/TrEMBL
      Q658J0
      Conserved Domains (1) summary
      pfam01784
      Location:33 → 354
      NIF3; NIF3 (NGG1p interacting factor 3)

    8. NM_001369445.2 → NP_001356374.1  NIF3-like protein 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC005037
      Consensus CDS
      CCDS46485.1
      UniProtKB/Swiss-Prot
      Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
      UniProtKB/TrEMBL
      Q658J0
      Conserved Domains (1) summary
      pfam01784
      Location:33 → 354
      NIF3; NIF3 (NGG1p interacting factor 3)

    9. NM_021824.3 → NP_068596.2  NIF3-like protein 1 isoform 2

      See identical proteins and their annotated locations for NP_068596.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and uses a downstream in-frame translation initiation codon, compared to variant 1. The resulting isoform (2) is shorter at the N-terminus, compared to isoform 1. Both variants 2 and 3 encode the same isoform.
      Source sequence(s)
      AB038949, BG724012, BM974977
      Consensus CDS
      CCDS42797.1
      UniProtKB/TrEMBL
      Q658J0
      Related
      ENSP00000352711.4, ENST00000359683.8
      Conserved Domains (1) summary
      pfam01784
      Location:6 → 327
      NIF3; NIF3 (NGG1p interacting factor 3)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      200889327..200903932
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445371.1 → XP_047301327.1  NIF3-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
      UniProtKB/TrEMBL
      Q658J0

    2. XM_047445372.1 → XP_047301328.1  NIF3-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
      UniProtKB/TrEMBL
      Q658J0

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      201372777..201387382
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343274.1 → XP_054199249.1  NIF3-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
      UniProtKB/TrEMBL
      Q658J0

    2. XM_054343273.1 → XP_054199248.1  NIF3-like protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q53TX4, Q6X735, Q9GZT8, Q9H2D2, Q9HC18
      UniProtKB/TrEMBL
      Q658J0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9GZT8.2 GenPept UniProtKB/Swiss-Prot:Q9GZT8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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