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

Gene ID: 100978, updated on 21-Apr-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 transcription, DNA-templated. 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, Apr 2022]
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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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 (18) 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)
  • Targeted (1) 
  • Endonuclease-mediated (2) 

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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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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