LXL04_005894 | RubberDandelionOmics

Gene overview

LXL04_005894

Reference: OH-1004 Chr: Chr01 Coordinates: 175285367-175289438 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2973 bp · LXL04_005894|LXL04_005894|OH1004|cDNA

ATGGCGACGAAGTTTTTATCATTGGCGTGTATACGTGTCACCGGCGCTACCGGCGACGGCTACTCCCGAGGATTATCACCGCGGCCGCACTATCCATCTATGCCGAAGTACCCAAAGGGAGTGTCGGCAGATATGGAGAGCAATATCGATAAATCGGAAAGTAGAGCTCTGTTTTCCGTCACCGGAATGACTTGCTCCGCCTGTGCCGGATCGGTGGAGAAGGCGGTGAAGCGGTTGCCGGGAATCAAGGAGGCTGTTAT...

CDS

Download CDS FASTA

2973 bp · LXL04_005894|LXL04_005894|OH1004|CDS

ATGGCGACGAAGTTTTTATCATTGGCGTGTATACGTGTCACCGGCGCTACCGGCGACGGCTACTCCCGAGGATTATCACCGCGGCCGCACTATCCATCTATGCCGAAGTACCCAAAGGGAGTGTCGGCAGATATGGAGAGCAATATCGATAAATCGGAAAGTAGAGCTCTGTTTTCCGTCACCGGAATGACTTGCTCCGCCTGTGCCGGATCGGTGGAGAAGGCGGTGAAGCGGTTGCCGGGAATCAAGGAGGCTGTTAT...

Protein

Download Protein FASTA

990 aa · LXL04_005894|LXL04_005894|OH1004|PROTEIN

MATKFLSLACIRVTGATGDGYSRGLSPRPHYPSMPKYPKGVSADMESNIDKSESRALFSVTGMTCSACAGSVEKAVKRLPGIKEAVIDVLNNRAQVMFYPSFINEETIRETIEDVGFEATLIMEKSNESTQVCRILIKGMTCTTCSTTVESALRSLHGVHKTQVALATEEAEIHYDPIIIHHEQLTNAIEDTGFEAILISTGEDVSKIDLQMDGLWNESFIKVIEQSLQALPGVEKIEIDPNLRKFSVSYKPDLTGPRSF...

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_005894`
TK1151 ID	TkA01G009220
OH-1004 ID	LXL04_005894
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.500
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_005894

Location Chr01:175285367-175289438 (+)

Description Similar to HMA5: Probable copper-transporting ATPase HMA5

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
`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
`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
`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_005894 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009636 response to toxic substance Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

GO:0010119 regulation of stomatal movement Biological Process

GO:0010273 detoxification of copper ion Biological Process

GO:0046688 response to copper ion Biological Process

GO:0055070 copper ion homeostasis Biological Process

GO:0055085 transmembrane transport Biological Process

GO:0071280 cellular response to copper ion Biological Process

GO:0005768 endosome Cellular Component

GO:0005774 vacuolar membrane Cellular Component

GO:0005794 Golgi apparatus Cellular Component

KEGG gene cross-reference

ath:AT1G63440

ath:AT5G44790

dosa:Os02g0196600

dosa:Os04g0556000

dosa:Os06g0665800

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.

Endoplasmic reticulum0.327

Rank 1 · LXL04_005894 · OH-1004

Cell membrane0.194

Rank 2 · LXL04_005894 · OH-1004

Cytoplasm0.175

Rank 3 · LXL04_005894 · OH-1004

Mitochondrion0.143

Rank 4 · LXL04_005894 · OH-1004

Golgi apparatus0.137

Rank 5 · LXL04_005894 · 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.

PF00403.33HMA58-118 aa

PF00403.33HMA135-195 aa

PF00403.33HMA222-268 aa

PF00122.26E1-E2_ATPase437-543 aa

PF00702.33Hydrolase653-875 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005894	`PF00403.33`	HMA	58	118	9.1e-39	132.4
LXL04_005894	`PF00403.33`	HMA	135	195	9.1e-39	132.4
LXL04_005894	`PF00403.33`	HMA	222	268	9.1e-39	132.4
LXL04_005894	`PF00122.26`	E1-E2_ATPase	437	543	9.5e-23	80.7
LXL04_005894	`PF00702.33`	Hydrolase	653	875	2.3e-34	120.2

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
`Q9SH30`	Arabidopsis thaliana	Probable copper-transporting ATPase HMA5	72.527%	Swiss-Prot	strong database homology
`Q9S7J8`	Arabidopsis thaliana	Copper-transporting ATPase RAN1	48.543%	Swiss-Prot	moderate database homology
`A3AWA4`	Oryza sativa subsp. japonica	Copper-transporting ATPase HMA5	68.637%	Swiss-Prot	strong database homology
`Q6H7M3`	Oryza sativa subsp. japonica	Copper-transporting ATPase HMA4	57.889%	Swiss-Prot	strong database homology
`A0A0P0X004`	Oryza sativa subsp. japonica	Cation-transporting ATPase HMA5	48.737%	Swiss-Prot	moderate database homology

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