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    Nfxl1 nuclear transcription factor, X-box binding-like 1 [ Mus musculus (house mouse) ]

    Gene ID: 100978, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Nfxl1provided by MGI
    Official Full Name
    nuclear transcription factor, X-box binding-like 1provided by MGI
    Primary source
    MGI:MGI:1923646
    See related
    Ensembl:ENSMUSG00000072889 AllianceGenome:MGI:1923646
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    GCF; TCF9; DNABF; Gm1058; 1700012H24Rik; D430033A06Rik
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be active in nucleus. Is expressed in brain. Orthologous to human NFXL1 (nuclear transcription factor, X-box binding like 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 9.0), limb E14.5 (RPKM 7.9) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Nfxl1 in Genome Data Viewer
    Location:
    5 C3.2; 5 38.44 cM
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (72670647..72717078, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (72513304..72559735, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene corin, serine peptidase Neighboring gene synaptonemal complex central element protein 2 pseudogene Neighboring gene predicted gene, 23712 Neighboring gene STARR-seq mESC enhancer starr_13365 Neighboring gene STARR-seq mESC enhancer starr_13366 Neighboring gene STARR-positive B cell enhancer mm9_chr5:72950846-72951147 Neighboring gene predicted gene, 34144 Neighboring gene zygote arrest 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo. Evsikov AV, et al. Genes Dev, 2006 Oct 1. PMID 17015433, Free PMC Article
    2. Construction of long-transcript enriched cDNA libraries from submicrogram amounts of total RNAs by a universal PCR amplification method. Piao Y, et al. Genome Res, 2001 Sep. PMID 11544199, Free PMC Article
    3. A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. Thompson CL, et al. Neuron, 2014 Jul 16. PMID 24952961, Free PMC Article
    4. GUDMAP: the genitourinary developmental molecular anatomy project. McMahon AP, et al. J Am Soc Nephrol, 2008 Apr. PMID 18287559
    5. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Tanaka TS, et al. Proc Natl Acad Sci U S A, 2000 Aug 1. PMID 10922068, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (1) 

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    NF-X1-type zinc finger protein NFXL1
    Names
    ovarian zinc finger protein

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001359837.1 → NP_001346766.1  NF-X1-type zinc finger protein NFXL1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC161529
      UniProtKB/TrEMBL
      Q3ULV1, Q9DAE1
      Related
      ENSMUST00000146761.2
      Conserved Domains (1) summary
      cd16697
      Location:165 → 222
      RING-CH-C4HC3_NFXL1; RING-CH finger, H2 subclass (C4HC3-type), found in nuclear transcription factor, X-box binding-like 1 (NFXL1) and similar proteins

    2. NM_133921.3 → NP_598682.2  NF-X1-type zinc finger protein NFXL1 isoform 1

      See identical proteins and their annotated locations for NP_598682.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC161529
      Consensus CDS
      CCDS39109.1
      UniProtKB/TrEMBL
      E9Q8I7
      Related
      ENSMUSP00000084467.6, ENSMUST00000087216.12
      Conserved Domains (2) summary
      cd06008
      Location:421 → 469
      NF-X1-zinc-finger; Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger ...
      cd16697
      Location:165 → 227
      RING-CH-C4HC3_NFXL1; RING-CH finger, H2 subclass (C4HC3-type), found in nuclear transcription factor, X-box binding-like 1 (NFXL1) and similar proteins

    RNA

    1. NR_153351.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate coding exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC161529, AK132320
      Related
      ENSMUST00000135318.8

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      72670647..72717078 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011240686.2 → XP_011238988.1  NF-X1-type zinc finger protein NFXL1 isoform X1

      See identical proteins and their annotated locations for XP_011238988.1

      UniProtKB/TrEMBL
      E9Q8I7
      Conserved Domains (2) summary
      cd06008
      Location:421 → 469
      NF-X1-zinc-finger; Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger ...
      cd16697
      Location:165 → 227
      RING-CH-C4HC3_NFXL1; RING-CH finger, H2 subclass (C4HC3-type), found in nuclear transcription factor, X-box binding-like 1 (NFXL1) and similar proteins
    Nucleotide Protein Strain
    Heading Accession and Version

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