LXL04_028444 | RubberDandelionOmics

Gene overview

LXL04_028444

Reference: OH-1004 Chr: Chr06 Coordinates: 41953547-41960971 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2847 bp · LXL04_028444|LXL04_028444|OH1004|cDNA

ATGAAAGAAGATGCGCCAAATGATTTGCAAAAAAGCTATTTCGATGTGTTGGGATTATGTTGTTCATCGGAGGTACCACTTATCGAGAAGATCCTTAAACCTCTTGAAGGTGTTCACCATGTCTCCGTCATCGTTCCTTCCAGAACTGTAATTGTGCTTCACGACGCGGCCCTCATTTCTCAGTTTCAAATCGTTAAGGCGCTAAACCAAGCACGATTGGAAGCAAATGTGAGGATGAAAGGAGTTCAAAGCTACGGGAA...

CDS

Download CDS FASTA

2847 bp · LXL04_028444|LXL04_028444|OH1004|CDS

ATGAAAGAAGATGCGCCAAATGATTTGCAAAAAAGCTATTTCGATGTGTTGGGATTATGTTGTTCATCGGAGGTACCACTTATCGAGAAGATCCTTAAACCTCTTGAAGGTGTTCACCATGTCTCCGTCATCGTTCCTTCCAGAACTGTAATTGTGCTTCACGACGCGGCCCTCATTTCTCAGTTTCAAATCGTTAAGGCGCTAAACCAAGCACGATTGGAAGCAAATGTGAGGATGAAAGGAGTTCAAAGCTACGGGAA...

Protein

Download Protein FASTA

948 aa · LXL04_028444|LXL04_028444|OH1004|PROTEIN

MKEDAPNDLQKSYFDVLGLCCSSEVPLIEKILKPLEGVHHVSVIVPSRTVIVLHDAALISQFQIVKALNQARLEANVRMKGVQSYGNKWPSPYAVVCGVLLLLSFLKYVYSPFKWLALGAVAVGIIPLTLKAVASIRIFRFDINVLMLIAVGGSIFLKDYWEAGTIVFLLTISEWLETRASHKATAVMSSLMTIAPQKAVLADTGEEVNANEVKVNTRLAVKAGTMIPIDGIVVEGKCEVDEKALTGESFPVCKQVDSIV...

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_028444`
TK1151 ID	TkA07G156820
OH-1004 ID	LXL04_028444
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.100
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_028444

Location Chr06:41953547-41960971 (-)

Description Similar to HMA2: Cadmium/zinc-transporting ATPase HMA2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g30110`	Plays an important role in zinc transport and homeostasis.	P-type ATPase heavy metal transporters with roles in essential zinc homeostasis in Arabidopsis.2004 · DOI: 10.1105/tpc.020487
`At2g19110`	Involved in cadmium/zinc transport.	No verified direct reference in this release
`UniProt: P0CW78`	In a heterologous system, involved in cadmium and lead transport, but not in zinc transport.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0700700`	Zinc/cadmium transporter that plays an essential role in promoting translocation of zinc and cadmium from roots to shoots.	Cadmium retention in rice roots is influenced by cadmium availability, chelation and translocation.2011 · DOI: 10.1111/j.1365-3040.2011.02299.x Mutations in rice (Oryza sativa) heavy metal ATPase 2 (OsHMA2) restrict the translocation of zinc and cadmium.2012 · DOI: 10.1093/pcp/pcr166 The OsHMA2 transporter is involved in root-to-shoot translocation of Zn and Cd in rice.2012 · DOI: 10.1111/j.1365-3040.2012.02527.x Preferential delivery of zinc to developing tissues in rice is mediated by P-type heavy metal ATPase OsHMA2.2013 · DOI: 10.1104/pp.113.216564
`Os07g0232900`	Root-specific cadmium (Cd) transporter that mediates Cd efflux in root vacuoles.	Gene limiting cadmium accumulation in rice.2010 · DOI: 10.1073/pnas.1005396107 OsHMA3, a P1B-type of ATPase affects root-to-shoot cadmium translocation in rice by mediating efflux into vacuoles.2011 · DOI: 10.1111/j.1469-8137.2010.03459.x Overexpression of OsHMA3 enhances Cd tolerance and expression of Zn transporter genes in rice.2014 · DOI: 10.1093/jxb/eru340

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_028444 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006829 zinc ion transport Biological Process

GO:0006882 intracellular zinc ion homeostasis Biological Process

GO:0010038 response to metal ion Biological Process

GO:0010043 response to zinc ion Biological Process

GO:0015691 cadmium ion transport Biological Process

GO:0030001 metal ion transport Biological Process

GO:0032025 response to cobalt ion Biological Process

GO:0046686 response to cadmium ion Biological Process

GO:0055085 transmembrane transport Biological Process

GO:0071585 detoxification of cadmium ion Biological Process

GO:0005774 vacuolar membrane Cellular Component

GO:0005886 plasma membrane Cellular Component

KEGG gene cross-reference

ath:AT2G19110

ath:AT4G30110

dosa:Os06g0700650

dosa:Os07g0232900

osa:4342783

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.

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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 reticulum0.312

Rank 1 · LXL04_028444 · OH-1004

Cell membrane0.299

Rank 2 · LXL04_028444 · OH-1004

Cytoplasm0.222

Rank 3 · LXL04_028444 · OH-1004

Golgi apparatus0.159

Rank 4 · LXL04_028444 · OH-1004

Lysosome / Vacuole0.122

Rank 5 · LXL04_028444 · 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.

PF00122.26E1-E2_ATPase202-292 aa

PF00702.33Hydrolase389-603 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028444	`PF00122.26`	E1-E2_ATPase	202	292	1.2e-21	77.2
LXL04_028444	`PF00702.33`	Hydrolase	389	603	6.4e-29	102.4

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
`Q9SZW4`	Arabidopsis thaliana	Cadmium/zinc-transporting ATPase HMA2	55.067%	Swiss-Prot	strong database homology
`O64474`	Arabidopsis thaliana	Putative cadmium/zinc-transporting ATPase HMA4	60.826%	Swiss-Prot	strong database homology
`P0CW78`	Arabidopsis thaliana	Cadmium/zinc-transporting ATPase HMA3	62.034%	Swiss-Prot	strong database homology
`A3BF39`	Oryza sativa subsp. japonica	Cadmium/zinc-transporting ATPase HMA2	61.623%	Swiss-Prot	strong database homology
`Q8H384`	Oryza sativa subsp. japonica	Cadmium/zinc-transporting ATPase HMA3	56.377%	Swiss-Prot	strong database homology

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