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Nfx1 nuclear transcription factor, X-box binding 1 [ Mus musculus (house mouse) ]

Gene ID: 74164, updated on 11-Apr-2024

Summary

Official Symbol
Nfx1provided by MGI
Official Full Name
nuclear transcription factor, X-box binding 1provided by MGI
Primary source
MGI:MGI:1921414
See related
Ensembl:ENSMUSG00000028423 AllianceGenome:MGI:1921414
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
NFX.1; Tex42; TEG-42; 1300017N15Rik; 3000003M19Rik
Summary
Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and ubiquitin protein ligase activity. Acts upstream of or within negative regulation of MHC class II biosynthetic process and negative regulation of transcription by RNA polymerase II. Predicted to be located in cytosol; nuclear lumen; and plasma membrane. Predicted to be active in nucleus. Is expressed in several structures, including gut; hemolymphoid system gland; integumental system; male reproductive system; and urinary system. Orthologous to human NFX1 (nuclear transcription factor, X-box binding 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E18 (RPKM 14.2), CNS E14 (RPKM 14.2) and 28 other tissues See more
Orthologs
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Genomic context

See Nfx1 in Genome Data Viewer
Location:
4 A5; 4 20.72 cM
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (40970906..41025992)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (40970906..41025992)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:40895401-40895689 Neighboring gene BCL2-associated athanogene 1 Neighboring gene charged multivesicular body protein 5 Neighboring gene STARR-positive B cell enhancer ABC_E3485 Neighboring gene predicted gene, 52692 Neighboring gene microRNA 3094 Neighboring gene aquaporin 7 Neighboring gene predicted gene, 25637

Genomic regions, transcripts, and products

Expression

  • 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

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
enables ubiquitin protein ligase activity ISO
Inferred from Sequence Orthology
more info
 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
transcriptional repressor NF-X1
Names
nuclear transcription factor, X box-binding protein 1
testis expressed gene 42
NP_001277377.1
NP_001277378.1
NP_076228.2
XP_006538382.1
XP_011248425.1
XP_011248426.1

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_001290448.1NP_001277377.1  transcriptional repressor NF-X1 isoform 2

    See identical proteins and their annotated locations for NP_001277377.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks several exons in the 3' region and uses an alternate 3' exon structure, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK033850, AK146108, AW050319, CK388342
    Consensus CDS
    CCDS71360.1
    UniProtKB/Swiss-Prot
    B1AY10
    Related
    ENSMUSP00000030133.9, ENSMUST00000030133.15
    Conserved Domains (1) summary
    cd06008
    Location:616668
    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 ...
  2. NM_001290449.1NP_001277378.1  transcriptional repressor NF-X1 isoform 3

    See identical proteins and their annotated locations for NP_001277378.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks several exons in the 3' region and uses an alternate 3' exon structure, compared to variant 1. It encodes isoform 3, which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK033850, AK146108, AW050319, CK388342
    Consensus CDS
    CCDS71359.1
    UniProtKB/Swiss-Prot
    B1AY10
    Related
    ENSMUSP00000089203.7, ENSMUST00000091614.7
    Conserved Domains (1) summary
    cd06008
    Location:616668
    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 ...
  3. NM_023739.3NP_076228.2  transcriptional repressor NF-X1 isoform 1

    See identical proteins and their annotated locations for NP_076228.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF223576, AK013866, AK144647, BY309016
    Consensus CDS
    CCDS18054.1
    UniProtKB/Swiss-Prot
    B1AY10, Q3U2A7, Q3UK95, Q3UMW1, Q7TPT4, Q8CC59, Q9DBC8, Q9JKW7
    Related
    ENSMUSP00000095747.5, ENSMUST00000098143.11
    Conserved Domains (2) summary
    cd02643
    Location:9811054
    R3H_NF-X1; R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown ...
    cd06008
    Location:616668
    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 ...

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_000070.7 Reference GRCm39 C57BL/6J

    Range
    40970906..41025992
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006538319.5XP_006538382.1  transcriptional repressor NF-X1 isoform X3

    Conserved Domains (2) summary
    cd06008
    Location:616668
    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 ...
    cd16696
    Location:350403
    RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins
  2. XM_011250123.4XP_011248425.1  transcriptional repressor NF-X1 isoform X1

    Conserved Domains (2) summary
    cd06008
    Location:616668
    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 ...
    cd16696
    Location:350403
    RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins
  3. XM_011250124.4XP_011248426.1  transcriptional repressor NF-X1 isoform X2

    Conserved Domains (2) summary
    cd06008
    Location:616668
    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 ...
    cd16696
    Location:350403
    RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins