LXL04_005453 | RubberDandelionOmics

Gene overview

LXL04_005453

Reference: OH-1004 Chr: Chr01 Coordinates: 164360765-164375008 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5284 bp · LXL04_005453|LXL04_005453|OH1004|cDNA

ATGACAGTATTAGAAATTTGTCGACATCAAGCAATGGTAGGAAGATGGCGGCATAATAATGAAGTGGAGCTGATTTCTAAACATGATAACAACATCATGGCATCAAAGATAGGCAAAGTAACAGCAAATGGTCACAGATTTATTCTCAATTCAAAGAAGAAGGCATTCACTCAATCCAAAACCCAAATAGTCAACAACAGGTCTTTGACTTTAAAGCCCACATTTCAAAAACTTGGAAAAAGAAAAAGGTCAAACAAATG...

CDS

Download CDS FASTA

5271 bp · LXL04_005453|LXL04_005453|OH1004|CDS

ATGACAGTATTAGAAATTTGTCGACATCAAGCAATGGTAGGAAGATGGCGGCATAATAATGAAGTGGAGCTGATTTCTAAACATGATAACAACATCATGGCATCAAAGATAGGCAAAGTAACAGCAAATGGTCACAGATTTATTCTCAATTCAAAGAAGAAGGCATTCACTCAATCCAAAACCCAAATAGTCAACAACAGGTCTTTGACTTTAAAGCCCACATTTCAAAAACTTGGAAAAAGAAAAAGGTCAAACAAATG...

Protein

Download Protein FASTA

1756 aa · LXL04_005453|LXL04_005453|OH1004|PROTEIN

MTVLEICRHQAMVGRWRHNNEVELISKHDNNIMASKIGKVTANGHRFILNSKKKAFTQSKTQIVNNRSLTLKPTFQKLGKRKRSNKCSSCSRTTTTLLKNYSNFIKSGPPQRLLFSQDGQWVDFPQEVVDLVKDDFCSKKAAIEVKVNGAHFMLQIVYMIQIDLKTGAQKPIAWIDDKGTCVFPEINATCHGSHDDVDLGESSLTPEIKLHLEIEVNGVNSNSNNKFDECMGESIVKRIKFDQESQSQRKVVNDEIAPQK...

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_005453`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_005453

Location Chr01:164360765-164375008 (+)

Description Similar to SKL2: Probable inactive shikimate kinase like 2, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g35500`	Probable inactive shikimate kinase like 2, chloroplastic.	No verified direct reference in this release
`At1g33520`	Required for innate and induced resistance to pathogens such as compatible and incompatible isolates of P.syringae and P.parasitica.	MOS2, a protein containing G-patch and KOW motifs, is essential for innate immunity in Arabidopsis thaliana.2005 · DOI: 10.1016/j.cub.2005.09.038
`At1g32230`	Inactive ADP-ribosyltransferase that functions with SRO1 to regulate oxidative stress, hormonal and developmental responses.	CEO1, a new protein from Arabidopsis thaliana, protects yeast against oxidative damage.2000 · DOI: 10.1016/s0014-5793(00)02016-0 Ozone-sensitive arabidopsis rcd1 mutant reveals opposite roles for ethylene and jasmonate signaling pathways in regulating superoxide-dependent cell death.2000 · DOI: 10.1105/tpc.12.10.1849 A methyl viologen-resistant mutant of Arabidopsis, which is allelic to ozone-sensitive rcd1, is tolerant to supplemental ultraviolet-B irradiation.2004 · DOI: 10.1104/pp.103.033480 Arabidopsis RADICAL-INDUCED CELL DEATH1 belongs to the WWE protein-protein interaction domain protein family and modulates abscisic acid, ethylene, and methyl jasmonate responses.2004 · DOI: 10.1105/tpc.021832 Ozone-induced programmed cell death in the Arabidopsis radical-induced cell death1 mutant.2005 · DOI: 10.1104/pp.104.055681 Overexpression of the RADICAL-INDUCED CELL DEATH1 (RCD1) gene of Arabidopsis causes weak rcd1 phenotype with compromised oxidative-stress responses.2006 · DOI: 10.1271/bbb.50673 Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors.2009 · DOI: 10.1111/j.1365-313x.2009.03951.x The paralogous genes RADICAL-INDUCED CELL DEATH1 and SIMILAR TO RCD ONE1 have partially redundant functions during Arabidopsis development.2009 · DOI: 10.1104/pp.109.142786 RCD1 and SRO1 are necessary to maintain meristematic fate in Arabidopsis thaliana.2011 · DOI: 10.1093/jxb/erq363
`At2g35510`	Probable inactive ADP-ribosyltransferase that functions with RCD1 to regulate oxidative stress, hormonal and developmental responses.	Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors.2009 · DOI: 10.1111/j.1365-313x.2009.03951.x The paralogous genes RADICAL-INDUCED CELL DEATH1 and SIMILAR TO RCD ONE1 have partially redundant functions during Arabidopsis development.2009 · DOI: 10.1104/pp.109.142786 RCD1 and SRO1 are necessary to maintain meristematic fate in Arabidopsis thaliana.2011 · DOI: 10.1093/jxb/erq363
`At1g23550`	Probable inactive ADP-ribosyltransferase that may be involved in stress and developmental responses.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005453 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000303 response to superoxide Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0002758 innate immune response-activating signaling pathway Biological Process

GO:0006809 nitric oxide biosynthetic process Biological Process

GO:0006950 response to stress Biological Process

GO:0006970 response to osmotic stress Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0009073 aromatic amino acid family biosynthetic process Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

KEGG gene cross-reference

ath:AT1G32230

ath:AT1G33520

ath:AT2G35500

ath:AT2G35510

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.

Nucleus0.655

Rank 1 · LXL04_005453 · OH-1004

Cytoplasm0.302

Rank 2 · LXL04_005453 · OH-1004

Cell membrane0.078

Rank 3 · LXL04_005453 · OH-1004

Endoplasmic reticulum0.057

Rank 4 · LXL04_005453 · OH-1004

Plastid0.048

Rank 5 · LXL04_005453 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF23467.2WWE_5104-183 aa

PF12174.14RST485-549 aa

PF12656.13G-patch_21139-1196 aa

PF25088.2GPKOW_C1280-1387 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005453	`PF23467.2`	WWE_5	104	183	6.9e-32	110.6
LXL04_005453	`PF12174.14`	RST	485	549	8.7e-21	74.3
LXL04_005453	`PF12656.13`	G-patch_2	1139	1196	2.4e-18	66.6
LXL04_005453	`PF25088.2`	GPKOW_C	1280	1387	9.1e-37	126.2

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.

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Protein	Organism	Description	Identity	Database	Confidence
`O82290`	Arabidopsis thaliana	Probable inactive shikimate kinase like 2, chloroplastic	61.059%	Swiss-Prot	weak database homology
`Q9C801`	Arabidopsis thaliana	Protein MOS2	44.731%	Swiss-Prot	weak database homology
`Q8RY59`	Arabidopsis thaliana	Inactive poly [ADP-ribose] polymerase RCD1	36.111%	Swiss-Prot	weak database homology
`O82289`	Arabidopsis thaliana	Probable inactive poly [ADP-ribose] polymerase SRO1	32.286%	Swiss-Prot	weak database homology
`Q9ZUD9`	Arabidopsis thaliana	Probable inactive poly [ADP-ribose] polymerase SRO2	30.822%	Swiss-Prot	weak database homology

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