LXL04_004428 | RubberDandelionOmics

Gene overview

LXL04_004428

Reference: OH-1004 Chr: Chr01 Coordinates: 135645646-135650497 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2646 bp · LXL04_004428|LXL04_004428|OH1004|cDNA

ATGGACGTTAATGGGAGAGAAGATCTAAACAGACCATTTCTGCAAGAAGCCATGGAAGTTGCAGGTATTAAAATCACCGAGTTTCCAGATCAAGAGATAGCAGTATGCCGCCTCAAAATCAAGGGAATGACGTGCACAAGTTGCTCTGAATCGATTGAAACCTCTCTTTTAATGGTGGAAGGAGTGAAAAAGGCTGTCGTGGGTTTAGCTCTTGAAGAAGCAAAGATAAACTACGATCCAAATGTCACAAATACAACTAA...

CDS

Download CDS FASTA

2646 bp · LXL04_004428|LXL04_004428|OH1004|CDS

ATGGACGTTAATGGGAGAGAAGATCTAAACAGACCATTTCTGCAAGAAGCCATGGAAGTTGCAGGTATTAAAATCACCGAGTTTCCAGATCAAGAGATAGCAGTATGCCGCCTCAAAATCAAGGGAATGACGTGCACAAGTTGCTCTGAATCGATTGAAACCTCTCTTTTAATGGTGGAAGGAGTGAAAAAGGCTGTCGTGGGTTTAGCTCTTGAAGAAGCAAAGATAAACTACGATCCAAATGTCACAAATACAACTAA...

Protein

Download Protein FASTA

881 aa · LXL04_004428|LXL04_004428|OH1004|PROTEIN

MDVNGREDLNRPFLQEAMEVAGIKITEFPDQEIAVCRLKIKGMTCTSCSESIETSLLMVEGVKKAVVGLALEEAKINYDPNVTNTTKIIEAIVDAGFEADPIGPEIDANKVHIKLEGITIISSEDMAAIKQSMELLNGVNHVETNREECKLTVSYDPNLTGPRSVISFISDRYQARLYIPERKRDTERNHEIKMYRNLFFWSCLFSIPVFVFSMVLPMIPPYGNWLSYKIHNMLTIGMVSRWILCTPVQFFIGRRFYVGS...

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_004428`
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_004428

Location Chr01:135645646-135650497 (+)

Description Similar to HMA4: Copper-transporting ATPase HMA4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g63440`	Involved in copper import into the cell.	The Arabidopsis heavy metal P-type ATPase HMA5 interacts with metallochaperones and functions in copper detoxification of roots.2006 · DOI: 10.1111/j.1365-313x.2005.02601.x
`At5g44790`	Involved in copper import into the cell.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0196600`	Copper (Cu) transporter that mediates Cu transport in root vacuoles.	A heavy metal P-type ATPase OsHMA4 prevents copper accumulation in rice grain.2016 · DOI: 10.1038/ncomms12138
`Os04g0556000`	Copper (Cu) transporter that plays an essential role in promoting translocation of Cu from roots to shoots.	A member of the heavy metal P-type ATPase OsHMA5 is involved in xylem loading of copper in rice.2013 · DOI: 10.1104/pp.113.226225
`Os06g0665800`	Metal efflux transporter that may play a role in detoxification of heavy metals, such as zinc, copper, lead and cadmium, especially in the shoots.	Rice P1B-type heavy-metal ATPase, OsHMA9, is a metal efflux protein.2007 · DOI: 10.1104/pp.107.102236

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004428 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0010273 detoxification of copper ion Biological Process

GO:0046688 response to copper ion Biological Process

GO:0055085 transmembrane transport Biological Process

GO:0071280 cellular response to copper ion Biological Process

GO:0005774 vacuolar membrane Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0005507 copper ion binding Molecular Function

GO:0005524 ATP binding Molecular Function

GO:0016887 ATP hydrolysis activity Molecular Function

GO:0140581 P-type monovalent copper transporter activity Molecular Function

KEGG gene cross-reference

ath:AT1G63440

dosa:Os02g0196600

dosa:Os04g0556000

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 membrane0.317

Rank 1 · LXL04_004428 · OH-1004

Endoplasmic reticulum0.255

Rank 2 · LXL04_004428 · OH-1004

Cytoplasm0.174

Rank 3 · LXL04_004428 · OH-1004

Golgi apparatus0.149

Rank 4 · LXL04_004428 · OH-1004

Lysosome / Vacuole0.147

Rank 5 · LXL04_004428 · 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.

PF00403.33HMA38-98 aa

PF00122.26E1-E2_ATPase358-445 aa

PF00702.33Hydrolase555-775 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004428	`PF00403.33`	HMA	38	98	6.6e-17	62.4
LXL04_004428	`PF00122.26`	E1-E2_ATPase	358	445	9.2e-22	77.5
LXL04_004428	`PF00702.33`	Hydrolase	555	775	4.7e-31	109.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SH30`	Arabidopsis thaliana	Probable copper-transporting ATPase HMA5	57.355%	Swiss-Prot	strong database homology
`Q9S7J8`	Arabidopsis thaliana	Copper-transporting ATPase RAN1	48.703%	Swiss-Prot	moderate database homology
`Q6H7M3`	Oryza sativa subsp. japonica	Copper-transporting ATPase HMA4	68.249%	Swiss-Prot	strong database homology
`A3AWA4`	Oryza sativa subsp. japonica	Copper-transporting ATPase HMA5	56.075%	Swiss-Prot	strong database homology
`A0A0P0X004`	Oryza sativa subsp. japonica	Cation-transporting ATPase HMA5	48.434%	Swiss-Prot	moderate database homology

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