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    Nif3l1 NGG1 interacting factor 3 like 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 301431, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Nif3l1provided by RGD
    Official Full Name
    NGG1 interacting factor 3 like 1provided by RGD
    Primary source
    RGD:1310329
    See related
    EnsemblRapid:ENSRNOG00000013446 AllianceGenome:RGD:1310329
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable RNA polymerase II-specific DNA-binding transcription factor binding activity and identical protein binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II; neuron differentiation; and positive regulation of DNA-templated transcription. Predicted to be located in nucleus. Predicted to be active in mitochondrion. Orthologous to human NIF3L1 (NGG1 interacting factor 3 like 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Adrenal (RPKM 46.4), Kidney (RPKM 40.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Nif3l1 in Genome Data Viewer
    Location:
    9q31
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (67474286..67494350)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (59980101..60001490)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (65329143..65349280)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134480578 Neighboring gene CDC-like kinase 1 Neighboring gene peptidylprolyl isomerase like 3 Neighboring gene U2 spliceosomal RNA Neighboring gene origin recognition complex, subunit 2 Neighboring gene hyccin PI4KA lipid kinase complex subunit 2 Neighboring gene BAF nuclear assembly factor 1, pseudogene 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    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. 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
    4. Isolation and characterization of a novel human gene, NIF3L1, and its mouse ortholog, Nif3l1, highly conserved from bacteria to mammals. Tascou S, et al. Cytogenet Cell Genet, 2000. PMID 11124544
    5. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Fragoza R, et al. Nat Commun, 2019 Sep 12. PMID 31515488, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA polymerase II-specific DNA-binding transcription factor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    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-like 1
    Ngg1 interacting factor 3-like 1
    putative GTP cyclohydrolase 1 type 2 Nif3l1
    NP_001019934.1
    NP_001380617.1
    XP_006245020.1
    XP_006245022.1
    XP_006245024.1
    XP_006245025.1
    XP_017451850.1
    XP_038939235.1
    XP_038939238.1
    XP_063123015.1
    XP_063123016.1

    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_001024763.2 → NP_001019934.1  NIF3-like protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001019934.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/TrEMBL
      A6IP70, Q4V8D5
      Related
      ENSRNOP00000055461.2, ENSRNOT00000058667.7
      Conserved Domains (1) summary
      pfam01784
      Location:32 → 199
      NIF3; NIF3 (NGG1p interacting factor 3)

    2. NM_001393688.1 → NP_001380617.1  NIF3-like protein 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/Swiss-Prot
      Q4V7D6
      UniProtKB/TrEMBL
      A0A8I6A868, A6IP71
      Conserved Domains (1) summary
      pfam01784
      Location:32 → 353
      NIF3; NIF3 (NGG1p interacting factor 3)

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086027.1 Reference GRCr8

      Range
      67474286..67494350
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006244958.4 → XP_006245020.1  NIF3-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006245020.1

      UniProtKB/TrEMBL
      A0A8I6A868, A0A8L2Q986
      Related
      ENSRNOP00000018014.5, ENSRNOT00000018014.8
      Conserved Domains (1) summary
      pfam01784
      Location:42 → 363
      NIF3; NIF3 (NGG1p interacting factor 3)

    2. XM_006244962.5 → XP_006245024.1  NIF3-like protein 1 isoform X2

      See identical proteins and their annotated locations for XP_006245024.1

      UniProtKB/Swiss-Prot
      Q4V7D6
      UniProtKB/TrEMBL
      A0A8I6A868, A6IP71
      Related
      ENSRNOP00000089215.1, ENSRNOT00000119712.2
      Conserved Domains (1) summary
      pfam01784
      Location:32 → 353
      NIF3; NIF3 (NGG1p interacting factor 3)

    3. XM_006244963.5 → XP_006245025.1  NIF3-like protein 1 isoform X4

      UniProtKB/TrEMBL
      A6IP70
      Conserved Domains (1) summary
      pfam01784
      Location:42 → 209
      NIF3; NIF3 (NGG1p interacting factor 3)

    4. XM_063266946.1 → XP_063123016.1  NIF3-like protein 1 isoform X4

    5. XM_063266945.1 → XP_063123015.1  NIF3-like protein 1 isoform X3

    6. XM_039083310.1 → XP_038939238.1  NIF3-like protein 1 isoform X5

      Conserved Domains (1) summary
      pfam01784
      Location:42 → 209
      NIF3; NIF3 (NGG1p interacting factor 3)

    7. XM_006244960.5 → XP_006245022.1  NIF3-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006245022.1

      UniProtKB/TrEMBL
      A0A8I6A868, A0A8L2Q986
      Conserved Domains (1) summary
      pfam01784
      Location:42 → 363
      NIF3; NIF3 (NGG1p interacting factor 3)

    8. XM_039083307.2 → XP_038939235.1  NIF3-like protein 1 isoform X2

      UniProtKB/Swiss-Prot
      Q4V7D6
      UniProtKB/TrEMBL
      A0A8I6A868, A6IP71
      Conserved Domains (1) summary
      pfam01784
      Location:32 → 353
      NIF3; NIF3 (NGG1p interacting factor 3)

    9. XM_017596361.3 → XP_017451850.1  NIF3-like protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A868, A0A8L2Q986
      Conserved Domains (1) summary
      pfam01784
      Location:42 → 363
      NIF3; NIF3 (NGG1p interacting factor 3)

    RNA

    1. XR_005488870.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q4V7D6.1 GenPept UniProtKB/Swiss-Prot:Q4V7D6

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