NFX1 nuclear transcription factor, X-box binding 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NFX1provided by HGNC
Official Full Name: nuclear transcription factor, X-box binding 1provided by HGNC
Primary source: HGNC:HGNC:7803
See related: Ensembl:ENSG00000086102 MIM:603255; AllianceGenome:HGNC:7803
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NFX2; Tex42; TEG-42
Summary: MHC class II gene expression is controlled primarily at the transcriptional level by transcription factors that bind to the X and Y boxes, two highly conserved elements in the proximal promoter of MHC class II genes. The protein encoded by this gene is a transcriptional repressor capable of binding to the conserved X box motif of HLA-DRA and other MHC class II genes in vitro. The protein may play a role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by IFN-gamma. Three alternative splice variants, each of which encodes a different isoform, have been identified. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in thyroid (RPKM 8.4), lymph node (RPKM 6.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9p13.3

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (33290516..33371157)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (33309149..33389758)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (33290514..33371155)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

High expression of NFX1-123 in HPV positive head and neck squamous cell carcinomas.
Title: High expression of NFX1-123 in HPV positive head and neck squamous cell carcinomas.
we found that NFX1-123 was a bona fide substrate of the deubiquitinase USP9X and that it could be degraded by the ubiquitin-proteasome system. The present study provided new insight into understanding the biological function of USP9X by targeting its substrate NFX1-123.
Title: Identification of a USP9X Substrate NFX1-123 by SILAC-Based Quantitative Proteomics.
initial mRNP binding to the NPC did not require NXF1 in the NPC, whereas release into the cytoplasm did. NXF1 localization in the NPC did not require RNA or RNA binding. Superresolution microscopy showed that NXF1 consistently occupied positions on the cytoplasmic side of the NPC.
Title: Imaging within single NPCs reveals NXF1's role in mRNA export on the cytoplasmic side of the pore.
Results indicate that NFX1-123 is markedly increased in cervical cancer, its greater expression in 16E6 expressing cells is associated with improved growth and telomerase activity, and that this association is maintained in HPV 16 positive cervical cancer cell lines.
Title: NFX1-123 is highly expressed in cervical cancer and increases growth and telomerase activity in HPV 16E6 expressing cells.
NFX1-123 in mediating epithelial differentiation through the JNK signaling pathway.
Title: HPV type 16 E6 and NFX1-123 augment JNK signaling to mediate keratinocyte differentiation and L1 expression.
This study identifies NFX1-123 as a critical host protein partner through which 16E6 is able to subvert the immune response and in turn permit a long-lived high-risk Human papillomavirus infection.
Title: Human papillomavirus type 16 E6 and NFX1-123 mislocalize immune signaling proteins and downregulate immune gene expression in keratinocytes.
The results showed that a repressor complex composed of NFX1-91, mSin3A and histone deacetylase 1 was involved in the PKC-delta-induced repression of the hTERT promoter, which resulted in the repression of hTERT transcription.
Title: Involvement of the NFX1-repressor complex in PKC-δ-induced repression of hTERT transcription.
Human papillomavirus 16 E6 (16E6) interacts with the cellular protein NFX1-123, and they collaboratively increase the growth and differentiation master regulator, Notch1.
Title: Human papillomavirus 16E6 and NFX1-123 potentiate Notch signaling and differentiation without activating cellular arrest.
NFX1-123 and human papillomavirus 16E6 upregulated Notch 1 expression in keratinocytes.
Title: NFX1-123 and human papillomavirus 16E6 increase Notch expression in keratinocytes.
a mechanism for HPV16 E6 activation of the NFkappaB pathway through NFX1-91
Title: NFX1 plays a role in human papillomavirus type 16 E6 activation of NFkappaB activity.

Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH75007 (e-PCR)
- UniSTS:86871

WI-22028 (e-PCR)
- UniSTS:79990

RH35865 (e-PCR)
- UniSTS:61820

STS-AA037854 (e-PCR)
- UniSTS:49053

RH118658 (e-PCR)
- UniSTS:138151

D9S1081 (e-PCR)
- UniSTS:56025

D9S1052E (e-PCR)
- UniSTS:151268

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase activity	TAS Traceable Author Statement more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in inflammatory response	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of MHC class II biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in protein autoubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	TAS Traceable Author Statement more info	PubMed
involved_in transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: transcriptional repressor NF-X1

Names: nuclear transcription factor, X box-binding protein 1

NP_001305687.1

EC 6.3.2.-

NP_002495.2

EC 6.3.2.-

NP_667345.1

EC 6.3.2.-

XP_047279383.1

EC 6.3.2.-

XP_047279384.1

EC 6.3.2.-

XP_047279385.1

EC 6.3.2.-

XP_054218977.1

EC 6.3.2.-

XP_054218978.1

EC 6.3.2.-

XP_054218979.1

EC 6.3.2.-

XP_054218980.1

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.

Genomic

NG_029578.1 RefSeqGene

Range

5097..85738

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001318758.2 → NP_001305687.1 transcriptional repressor NF-X1 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate in-frame splice site in an internal exon, compared to variant 1. It encodes isoform 4 which is longer than isoform 1.

Source sequence(s)

AI884552, AL356218, AL356472, AL832342, DA290058

Conserved Domains (2) summary

cd02643
Location:988 → 1061

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:622 → 674

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_002504.6 → NP_002495.2 transcriptional repressor NF-X1 isoform 1

See identical proteins and their annotated locations for NP_002495.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

BC012151, BP871782, DB076795

Consensus CDS

CCDS6538.1

UniProtKB/Swiss-Prot

A8K6H8, Q12986, Q5VXW6, Q96EL5, Q9BXI1

Related

ENSP00000368856.3, ENST00000379540.8

Conserved Domains (3) summary

cd02643
Location:987 → 1060

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:622 → 674

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:356 → 409

RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins
NM_147134.4 → NP_667345.1 transcriptional repressor NF-X1 isoform 3

See identical proteins and their annotated locations for NP_667345.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) utilizes an alternate 3' terminal exon compared to variant 1 and encodes the shortest isoform (3), with a unique C-terminus.

Source sequence(s)

AK225750, AL356472, DA290058, DB076795

Consensus CDS

CCDS6540.1

UniProtKB/TrEMBL

A0JLR2

Related

ENSP00000317695.6, ENST00000318524.6

Conserved Domains (2) summary

cd06008
Location:622 → 674

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:356 → 409

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

33290516..33371157

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047423427.1 → XP_047279383.1 transcriptional repressor NF-X1 isoform X1
XM_047423429.1 → XP_047279385.1 transcriptional repressor NF-X1 isoform X3

Conserved Domains (2) summary

cd06008
Location:622 → 674

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:356 → 409

RING-CH-C4HC3_NFX1; RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins
XM_047423428.1 → XP_047279384.1 transcriptional repressor NF-X1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

33309149..33389758

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054363002.1 → XP_054218977.1 transcriptional repressor NF-X1 isoform X1
XM_054363004.1 → XP_054218979.1 transcriptional repressor NF-X1 isoform X3
XM_054363003.1 → XP_054218978.1 transcriptional repressor NF-X1 isoform X2
XM_054363005.1 → XP_054218980.1 transcriptional repressor NF-X1 isoform X4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_147133.2: Suppressed sequence

Description

NM_147133.2: This RefSeq was removed because currently there is insufficient support for the transcript.