LXL04_038117 | RubberDandelionOmics

Gene overview

LXL04_038117

Reference: OH-1004 Chr: Chr09 Coordinates: 31692924-31696306 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1743 bp · LXL04_038117|LXL04_038117|OH1004|cDNA

ATGGTTTTGGATGCTTCAAAAGATGATACGGTTTCATTGGACTACAAAGGAAACCCGGCTGATAACTCAAAGACCGGTGGTTGGCTTGCAGCCGGGCTTATTTTAGGGACTGAGCTCTCTGAGAGAATATGTGTGATGGGAATATCGATGAATTTGGTGACATATTTGGTAGGGGAATTGCATCTTTCATCATCAAAATCAGCAAACACGGTGACAAATTTCATGGGAGCGTTGAACATTTTAGCGCTTTTTGGAGGGTT...

CDS

Download CDS FASTA

1743 bp · LXL04_038117|LXL04_038117|OH1004|CDS

ATGGTTTTGGATGCTTCAAAAGATGATACGGTTTCATTGGACTACAAAGGAAACCCGGCTGATAACTCAAAGACCGGTGGTTGGCTTGCAGCCGGGCTTATTTTAGGGACTGAGCTCTCTGAGAGAATATGTGTGATGGGAATATCGATGAATTTGGTGACATATTTGGTAGGGGAATTGCATCTTTCATCATCAAAATCAGCAAACACGGTGACAAATTTCATGGGAGCGTTGAACATTTTAGCGCTTTTTGGAGGGTT...

Protein

Download Protein FASTA

580 aa · LXL04_038117|LXL04_038117|OH1004|PROTEIN

MVLDASKDDTVSLDYKGNPADNSKTGGWLAAGLILGTELSERICVMGISMNLVTYLVGELHLSSSKSANTVTNFMGALNILALFGGFLADAKFGRYLTIAIFASICAVGVTLLTLATSIPGMRPPHCDSPRKNECIEASGSQLAMLYVALYTIALGGGGIKSNVSGFGSDQFDISDPKEEKKMVYFFNRFYFCVSLGSLFAVTILVYIQDNVGRGWGYGISAGTMILAVVVLVCGTMLYRFKKPQGSPLTVIWRVVFLAI...

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_038117`
TK1151 ID	TkA04G390560
OH-1004 ID	LXL04_038117
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	99.700
Protein coverage (%)	TK1151 100.000 / OH-1004 61.379 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
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_038117

Location Chr09:31692924-31696306 (+)

Description Similar to NPF6.4: Protein NRT1/ PTR FAMILY 6.4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g21670`	Low-affinity nitrate transporter.	No verified direct reference in this release
`At1g12110`	Dual affinity nitrate transporter.	CHL1 is a dual-affinity nitrate transporter of Arabidopsis involved in multiple phases of nitrate uptake.1999 · DOI: 10.1105/tpc.11.5.865 The nitrate transporter AtNRT1.1 (CHL1) functions in stomatal opening and contributes to drought susceptibility in Arabidopsis.2003 · DOI: 10.1105/tpc.006312 Switching between the two action modes of the dual-affinity nitrate transporter CHL1 by phosphorylation.2003 · DOI: 10.1093/emboj/cdg118 Transcript profiling in the chl1-5 mutant of Arabidopsis reveals a role of the nitrate transporter NRT1.1 in the regulation of another nitrate transporter, NRT2.1.2004 · DOI: 10.1105/tpc.104.024380 The Arabidopsis NRT1.1 transporter participates in the signaling pathway triggering root colonization of nitrate-rich patches.2006 · DOI: 10.1073/pnas.0605275103 A genetic screen for nitrate regulatory mutants captures the nitrate transporter gene NRT1.1.2009 · DOI: 10.1104/pp.109.140434 Nitrate-regulated auxin transport by NRT1.1 defines a mechanism for nutrient sensing in plants.2010 · DOI: 10.1016/j.devcel.2010.05.008 The herbicide sensitivity gene CHL1 of Arabidopsis encodes a nitrate-inducible nitrate transporter.1993 · DOI: 10.1016/0092-8674(93)90399-b The Arabidopsis CHL1 protein plays a major role in high-affinity nitrate uptake.1998 · DOI: 10.1073/pnas.95.25.15134
`At2g26690`	Low-affinity proton-dependent nitrate transporter.	No verified direct reference in this release
`At3g54140`	Peptide transporter.	AtPTR1, a plasma membrane peptide transporter expressed during seed germination and in vascular tissue of Arabidopsis.2004 · DOI: 10.1111/j.1365-313x.2004.02224.x AtPTR1 and AtPTR5 transport dipeptides in planta.2008 · DOI: 10.1104/pp.108.123844
`At5g01180`	Peptide transporter.	AtPTR1 and AtPTR5 transport dipeptides in planta.2008 · DOI: 10.1104/pp.108.123844

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038117 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006857 oligopeptide transport Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009611 response to wounding Biological Process

GO:0009635 response to herbicide Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009753 response to jasmonic acid Biological Process

GO:0009860 pollen tube growth Biological Process

GO:0010167 response to nitrate Biological Process

GO:0010540 basipetal auxin transport Biological Process

GO:0015031 protein transport Biological Process

GO:0015706 nitrate transmembrane transport Biological Process

GO:0042128 nitrate assimilation Biological Process

KEGG gene cross-reference

ath:AT1G12110

ath:AT2G26690

ath:AT3G21670

ath:AT3G54140

ath:AT5G01180

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 membrane0.800

Rank 1 · LXL04_038117 · OH-1004

Cytoplasm0.076

Rank 2 · LXL04_038117 · OH-1004

Endoplasmic reticulum0.074

Rank 3 · LXL04_038117 · OH-1004

Lysosome / Vacuole0.053

Rank 4 · LXL04_038117 · OH-1004

Mitochondrion0.030

Rank 5 · LXL04_038117 · 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_148-492 aa

PF00854.28PTR296-504 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038117	`PF07690.22`	MFS_1	48	492	3.2e-10	40.2
LXL04_038117	`PF00854.28`	PTR2	96	504	3e-105	353.1

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
`Q9LVE0`	Arabidopsis thaliana	Protein NRT1/ PTR FAMILY 6.4	68.148%	Swiss-Prot	strong database homology
`Q05085`	Arabidopsis thaliana	Protein NRT1/ PTR FAMILY 6.3	49.324%	Swiss-Prot	moderate database homology
`Q9SZY4`	Arabidopsis thaliana	Protein NRT1/ PTR FAMILY 6.2	50.712%	Swiss-Prot	strong database homology
`Q9M390`	Arabidopsis thaliana	Protein NRT1/ PTR FAMILY 8.1	42.376%	Swiss-Prot	moderate database homology
`Q9LFB8`	Arabidopsis thaliana	Protein NRT1/ PTR FAMILY 8.2	41.281%	Swiss-Prot	moderate database homology

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