LXL04_004581 | RubberDandelionOmics

Gene overview

LXL04_004581

Reference: OH-1004 Chr: Chr01 Coordinates: 140980457-140981419 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

963 bp · LXL04_004581|LXL04_004581|OH1004|cDNA

ATGGCGGCCCACCCAAACTACTGTTTCTCAAACACGTTTGAAGATGTTCTTGCATCCTCCCTACAATTACCAACCAACGATtccatcatcttcaacctctCGATCCTCAGAGACAAGTCCCAACAAGTTCAATCCATGGCCAACATGTTGTTCGCCCAAACACAAACTCAATCCATAGCCTCTAACTCAACCTCCATTAACATCGACAGCGTCGCCGGTTTGCTCCAAGAAATCATCGCGATAGCTTCTAACGTCATGTT...

CDS

Download CDS FASTA

963 bp · LXL04_004581|LXL04_004581|OH1004|CDS

ATGGCGGCCCACCCAAACTACTGTTTCTCAAACACGTTTGAAGATGTTCTTGCATCCTCCCTACAATTACCAACCAACGATTCCATCATCTTCAACCTCTCGATCCTCAGAGACAAGTCCCAACAAGTTCAATCCATGGCCAACATGTTGTTCGCCCAAACACAAACTCAATCCATAGCCTCTAACTCAACCTCCATTAACATCGACAGCGTCGCCGGTTTGCTCCAAGAAATCATCGCGATAGCTTCTAACGTCATGTT...

Protein

Download Protein FASTA

320 aa · LXL04_004581|LXL04_004581|OH1004|PROTEIN

MAAHPNYCFSNTFEDVLASSLQLPTNDSIIFNLSILRDKSQQVQSMANMLFAQTQTQSIASNSTSINIDSVAGLLQEIIAIASNVMFACQNIGITQIDNTYNNATLDFDQISQPTTMFKWSDGGIDQKTSGSVSFNTKNEETGLGYDYDIVEMDAADLLAKYTHYCQVCGKGFKRDANLRMHMRAHGDEYKSNAALANPMASNGGKKMKPARKYSCPQEGCRWNRKHEKFQPLKSMVCMKNHYKRSHCPKMYSCKRCQQK...

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_004581`
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_004581

Location Chr01:140980457-140981419 (+)

Description Similar to STOP2: Protein SENSITIVE TO PROTON RHIZOTOXICITY 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g22890`	Probable transcription factor.	STOP2 activates transcription of several genes for Al- and low pH-tolerance that are regulated by STOP1 in Arabidopsis.2014 · DOI: 10.1093/mp/sst116
`At1g34370`	Probable transcription factor.	Zinc finger protein STOP1 is critical for proton tolerance in Arabidopsis and coregulates a key gene in aluminum tolerance.2007 · DOI: 10.1073/pnas.0700117104 Aluminum-activated citrate and malate transporters from the MATE and ALMT families function independently to confer Arabidopsis aluminum tolerance.2009 · DOI: 10.1111/j.1365-313x.2008.03696.x STOP1 regulates multiple genes that protect arabidopsis from proton and aluminum toxicities.2009 · DOI: 10.1104/pp.108.134700 STOP2 activates transcription of several genes for Al- and low pH-tolerance that are regulated by STOP1 in Arabidopsis.2014 · DOI: 10.1093/mp/sst116
`At5g60470`	Probable transcription factor.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0871200`	Probable transcription factor that may be involved in aluminum tolerance.	No verified direct reference in this release
`Os12g0170400`	Transcriptional activator that regulates the expression of genes involved in aluminum (Al) tolerance.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004581 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0010044 response to aluminum ion Biological Process

GO:0010447 response to acidic pH Biological Process

GO:0042542 response to hydrogen peroxide Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0071453 cellular response to oxygen levels Biological Process

GO:0071472 cellular response to salt stress Biological Process

GO:1900037 regulation of cellular response to hypoxia Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

ath:AT1G34370

ath:AT5G22890

ath:AT5G60470

dosa:Os01g0871200

dosa:Os12g0170400

osa:4324940

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.

Nucleus0.977

Rank 1 · LXL04_004581 · OH-1004

Cytoplasm0.084

Rank 2 · LXL04_004581 · OH-1004

Cell membrane0.021

Rank 3 · LXL04_004581 · OH-1004

Endoplasmic reticulum0.013

Rank 4 · LXL04_004581 · OH-1004

Plastid0.010

Rank 5 · LXL04_004581 · 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.

PF23115.2zf-C2H2_STOP2_3rd214-248 aa

PF22995.3C2CH-3rd_BIRD-IDD252-276 aa

PF23118.3zf-C2H2_STOP2_C279-307 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004581	`PF23115.2`	zf-C2H2_STOP2_3rd	214	248	6.2e-22	78.0
LXL04_004581	`PF22995.3`	C2CH-3rd_BIRD-IDD	252	276	5.3e-06	26.7
LXL04_004581	`PF23118.3`	zf-C2H2_STOP2_C	279	307	3.8e-19	68.7

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
`Q0WT24`	Arabidopsis thaliana	Protein SENSITIVE TO PROTON RHIZOTOXICITY 2	50.637%	Swiss-Prot	strong database homology
`Q9C8N5`	Arabidopsis thaliana	Protein SENSITIVE TO PROTON RHIZOTOXICITY 1	39.329%	Swiss-Prot	moderate database homology
`F4JYZ8`	Arabidopsis thaliana	Protein indeterminate-domain 13	33.557%	Swiss-Prot	weak database homology
`Q943I6`	Oryza sativa subsp. japonica	Zinc finger protein STOP1 homolog	62.500%	Swiss-Prot	moderate database homology
`Q2QX40`	Oryza sativa subsp. japonica	Zinc finger protein STAR3	38.365%	Swiss-Prot	moderate database homology

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