LXL04_033020 | RubberDandelionOmics

Gene overview

LXL04_033020

Reference: OH-1004 Chr: Chr07 Coordinates: 33979976-33981942 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1694 bp · LXL04_033020|LXL04_033020|OH1004|cDNA

ACAGCTTACCGTTTCTTAGCTTATATCGTATATATATCATATACCTCTTCTCTATACGTTAATTTCTCTATTCCCCATATCTTTGGAGTTCAAAAACCAACAATGGCTTCCACTGACACAATCCCGGAGCATCAAGCAACCGTATCCATCCACAATGACGACACCACCACCTCTCCCCGGCGGACCTTCGCTCTGCCGGTGGATTCGGAAAACAAAGCTACACAGATGAAGGTGTTCTCGTTAGCACAACCCCACATGAG...

CDS

Download CDS FASTA

1572 bp · LXL04_033020|LXL04_033020|OH1004|CDS

ATGGCTTCCACTGACACAATCCCGGAGCATCAAGCAACCGTATCCATCCACAATGACGACACCACCACCTCTCCCCGGCGGACCTTCGCTCTGCCGGTGGATTCGGAAAACAAAGCTACACAGATGAAGGTGTTCTCGTTAGCACAACCCCACATGAGAGCCTTCCATCTATCATGGCTTTCCTTCTGCACTTGCGTTATATCCACCTTCGCCGCCGCCCCACTTGTTCCGATCATCCGGGACAACCTCAACCTCACCCG...

Protein

Download Protein FASTA

523 aa · LXL04_033020|LXL04_033020|OH1004|PROTEIN

MASTDTIPEHQATVSIHNDDTTTSPRRTFALPVDSENKATQMKVFSLAQPHMRAFHLSWLSFCTCVISTFAAAPLVPIIRDNLNLTRSDISNAGIASVSGSILSRLLMGVICDLVGPRYGCSVINILAAPVVFSVSFIADAGGYVAVRFMIGFSLATFVSCQYWTSVMFNGKIIGVVNGVSAGWGDLGGGLTQLLMPVLFHVITGMLGTTPFTAWRIAFFIPGWFHLIAGALVLMYGQDLPDGNFAEIYKEGRVAKDKFS...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_033020`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_033020

Location Chr07:33979976-33981942 (+)

Description Similar to NRT2.4: High affinity nitrate transporter 2.4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g60770`	Involved in high-affinity nitrate transport.	Disruption of the nitrate transporter genes AtNRT2.1 and AtNRT2.2 restricts growth at low external nitrate concentration.2004 · DOI: 10.1007/s00425-004-1266-x
`At1g08090`	Involved in nitrate transport, but does not seem to be able to mediate transport by its own.	Major alterations of the regulation of root NO(3)(-) uptake are associated with the mutation of Nrt2.1 and Nrt2.2 genes in Arabidopsis.2001 · DOI: 10.1104/pp.127.1.262 Disruption of the nitrate transporter genes AtNRT2.1 and AtNRT2.2 restricts growth at low external nitrate concentration.2004 · DOI: 10.1007/s00425-004-1266-x The putative high-affinity nitrate transporter NRT2.1 represses lateral root initiation in response to nutritional cues.2005 · DOI: 10.1073/pnas.0504219102 A central role for the nitrate transporter NRT2.1 in the integrated morphological and physiological responses of the root system to nitrogen limitation in Arabidopsis.2006 · DOI: 10.1104/pp.105.075721 Dissection of the AtNRT2.1:AtNRT2.2 inducible high-affinity nitrate transporter gene cluster.2007 · DOI: 10.1104/pp.106.091223 Nitrate signaling and the two component high affinity uptake system in Arabidopsis.2007 · DOI: 10.4161/psb.2.4.3870
`At3g45060`	Involved in high-affinity nitrate transport.	The NRT2.5 and NRT2.6 genes are involved in growth promotion of Arabidopsis by the plant growth-promoting rhizobacterium (PGPR) strain Phyllobacterium brassicacearum STM196.2013 · DOI: 10.1111/nph.12158
`At5g60780`	Involved in high-affinity nitrate transport.	No verified direct reference in this release
`At1g08100`	Involved in high-affinity nitrate transport.	Major alterations of the regulation of root NO(3)(-) uptake are associated with the mutation of Nrt2.1 and Nrt2.2 genes in Arabidopsis.2001 · DOI: 10.1104/pp.127.1.262 Disruption of the nitrate transporter genes AtNRT2.1 and AtNRT2.2 restricts growth at low external nitrate concentration.2004 · DOI: 10.1007/s00425-004-1266-x Dissection of the AtNRT2.1:AtNRT2.2 inducible high-affinity nitrate transporter gene cluster.2007 · DOI: 10.1104/pp.106.091223

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_033020 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0010167 response to nitrate Biological Process

GO:0015706 nitrate transmembrane transport Biological Process

GO:0042128 nitrate assimilation Biological Process

GO:0048527 lateral root development Biological Process

GO:0071249 cellular response to nitrate Biological Process

GO:0005886 plasma membrane Cellular Component

GO:0016020 membrane Cellular Component

GO:0015112 nitrate transmembrane transporter activity Molecular Function

KEGG gene cross-reference

ath:AT1G08090

ath:AT1G08100

ath:AT3G45060

ath:AT5G60770

ath:AT5G60780

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Cell membrane0.581

Rank 1 · LXL04_033020 · OH-1004

Cytoplasm0.159

Rank 2 · LXL04_033020 · OH-1004

Endoplasmic reticulum0.121

Rank 3 · LXL04_033020 · OH-1004

Lysosome / Vacuole0.118

Rank 4 · LXL04_033020 · OH-1004

Golgi apparatus0.072

Rank 5 · LXL04_033020 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF07690.22MFS_159-416 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_033020	`PF07690.22`	MFS_1	59	416	3.5e-19	69.6

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9FJH8`	Arabidopsis thaliana	High affinity nitrate transporter 2.4	65.370%	Swiss-Prot	strong database homology
`O82811`	Arabidopsis thaliana	High-affinity nitrate transporter 2.1	63.813%	Swiss-Prot	strong database homology
`Q9LXH0`	Arabidopsis thaliana	High affinity nitrate transporter 2.6	66.023%	Swiss-Prot	strong database homology
`Q9FJH7`	Arabidopsis thaliana	High affinity nitrate transporter 2.3	66.732%	Swiss-Prot	strong database homology
`Q9LMZ9`	Arabidopsis thaliana	High-affinity nitrate transporter 2.2	63.306%	Swiss-Prot	strong database homology

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