sequence-specific DNA binding transcription factor ATNDX [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Full Name: sequence-specific DNA binding transcription factor ATNDX
Primary source: TAIR:AT4G03090
Locus tag: AT4G03090
See related: Araport:AT4G03090
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Arabidopsis thaliana (ecotype: Columbia)
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as: AtNDX; NDX; Nodulin Homeobox; T4I9.3; T4I9_3
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Genomic context

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See in Genome Data Viewer

Location:: chromosome: 4

Exon count:: 17

Sequence:: Chromosome: 4; NC_003075.7 (1366053..1371557, complement)

Chromosome 4 - NC_003075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003075.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Arabidopsis Nodulin Homeobox Factor AtNDX Interacts with AtRING1A/B and Negatively Regulates Abscisic Acid Signaling.
Title: The Arabidopsis Nodulin Homeobox Factor AtNDX Interacts with AtRING1A/B and Negatively Regulates Abscisic Acid Signaling.
identified a homeodomain protein, AtNDX (At4g03090), that regulates COOLAIR, a set of antisense transcripts originating from the 3' end of Arabidopsis FLOWERING LOCUS C (FLC); R-loop stabilization mediated by AtNDX inhibits COOLAIR transcription, which in turn modifies FLC expression
Title: R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus.

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General gene information

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Homology

Orthologs from OrthoDB

NM_001340421.1

Supported by ESTs:

NM_116543.6

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded DNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in flower development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of antisense RNA transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within root development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within seed germination	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in mitochondrion	ISM Inferred from Sequence Model more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sequence-specific DNA binding transcription factor ATNDX

NP_001319856.1

sequence-specific DNA binding;sequence-specific DNA binding transcription factors; FUNCTIONS IN: sequence-specific DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: regulation of transcription, DNA-dependent; EXPRESSED IN: 12 plant structures; EXPRESSED DURING: 6 growth stages; CONTAINS InterPro DOMAIN/s: Homeobox (InterPro:IPR001356).

NP_192218.5

sequence-specific DNA binding;sequence-specific DNA binding transcription factors; FUNCTIONS IN: sequence-specific DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: regulation of transcription, DNA-dependent; EXPRESSED IN: 12 plant structures; EXPRESSED DURING: 6 growth stages; CONTAINS InterPro DOMAIN/s: Homeobox (InterPro:IPR001356); Has 162 Blast hits to 148 proteins in 59 species: Archae - 0; Bacteria - 10; Metazoa - 30; Fungi - 10; Plants - 59; Viruses - 0; Other Eukaryotes - 53 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NC_003075.7 Reference assembly

Range

1366053..1371557 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001340418.1 → NP_001319856.1 sequence-specific DNA binding transcription factor ATNDX [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8B7L9, A0A5S9XPE3, A0A7G2EVP5

Conserved Domains (1) summary

smart00389
Location:673 → 735

HOX; Homeodomain
NM_001340419.1 → NP_001329412.1 sequence-specific DNA binding transcription factor ATNDX [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8B7L9, A0A5S9XPE3, A0A7G2EVP5

Conserved Domains (1) summary

smart00389
Location:673 → 735

HOX; Homeodomain
NM_001340420.1 → NP_001329414.1 sequence-specific DNA binding transcription factor ATNDX [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8B7M1, A0A7G2EVP5
NM_116543.6 → NP_192218.5 sequence-specific DNA binding transcription factor ATNDX [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_192218.5

Status: REVIEWED

UniProtKB/Swiss-Prot

F4JI44, F4JI45, Q7GAL2, Q9ZTA5

UniProtKB/TrEMBL

A0A7G2EVP5

Conserved Domains (1) summary

smart00389
Location:698 → 760

HOX; Homeodomain
NM_001340421.1 → NP_001329413.1 sequence-specific DNA binding transcription factor ATNDX [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8B7M0, A0A7G2EVP5