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

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: human all
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Genomic context

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_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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

Process	Evidence Code	Pubs
acts_upstream_of_or_within negative regulation of MHC class II biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in protein autoubiquitination	ISO Inferred from Sequence Orthology 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

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Preferred Names: transcriptional repressor NF-X1

Names: nuclear transcription factor, X box-binding protein 1; testis expressed gene 42

NP_001277377.1

EC 6.3.2.-

NP_001277378.1

EC 6.3.2.-

NP_076228.2

EC 6.3.2.-

XP_006538382.1

EC 6.3.2.-

XP_011248425.1

EC 6.3.2.-

XP_011248426.1

EC 6.3.2.-

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)

NM_001290448.1 → NP_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:616 → 668

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 ...
NM_001290449.1 → NP_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:616 → 668

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 ...
NM_023739.3 → NP_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:981 → 1054

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:616 → 668

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

NC_000070.7 Reference GRCm39 C57BL/6J

Range

40970906..41025992

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (2) summary

cd06008
Location:616 → 668

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:350 → 403

RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins
XM_011250123.4 → XP_011248425.1 transcriptional repressor NF-X1 isoform X1

Conserved Domains (2) summary

cd06008
Location:616 → 668

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:350 → 403

RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins
XM_011250124.4 → XP_011248426.1 transcriptional repressor NF-X1 isoform X2

Conserved Domains (2) summary

cd06008
Location:616 → 668

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:350 → 403

RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins