LXL04_009990 | RubberDandelionOmics

Gene overview

LXL04_009990

Reference: OH-1004 Chr: Chr02 Coordinates: 137475957-137478998 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1155 bp · LXL04_009990|LXL04_009990|OH1004|cDNA

ATGGACGGTGATGGTTCTGTAGGTACATCATGTTTAATGGGGTTCGGAGATAACAACAACATCAATCAAAGCGGCAGTGGTAGTAATAATAACAACAGCATTGGATCCCTCTGTGCTCCTCCACCTCCTGTTATATACGGCAATTCTGTAATTTTTCCCACTCaggatcatcatcatcatcatcatcatcatcatcaaagCAACTGTGGTTCTTCAGCTATGATTCTCGAAGGCAACAATAGCAACATTAACGATGGAGG...

CDS

Download CDS FASTA

1155 bp · LXL04_009990|LXL04_009990|OH1004|CDS

ATGGACGGTGATGGTTCTGTAGGTACATCATGTTTAATGGGGTTCGGAGATAACAACAACATCAATCAAAGCGGCAGTGGTAGTAATAATAACAACAGCATTGGATCCCTCTGTGCTCCTCCACCTCCTGTTATATACGGCAATTCTGTAATTTTTCCCACTCAGGATCATCATCATCATCATCATCATCATCATCAAAGCAACTGTGGTTCTTCAGCTATGATTCTCGAAGGCAACAATAGCAACATTAACGATGGAGG...

Protein

Download Protein FASTA

384 aa · LXL04_009990|LXL04_009990|OH1004|PROTEIN

MDGDGSVGTSCLMGFGDNNNINQSGSGSNNNNSIGSLCAPPPPVIYGNSVIFPTQDHHHHHHHHHQSNCGSSAMILEGNNSNINDGGSLGFISSSSCSSSVKAKIMSHPHYPRLLSAYLNCQKIGAPPEVVERLEESCRASVMAAMSASSGYGGGCAGSTSGGGTGTTTVGQDPALDQFMEAYCEMLIKYEQELSKPFKEAMLFLSRIESQFKAISFSPSDSGLPSISFFISVCCGEGGMDRNGSSEEDLDVDVNNNNMV...

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_009990`
TK1151 ID	TkA03G488450
OH-1004 ID	LXL04_009990
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	95.600
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_009990

Location Chr02:137475957-137478998 (-)

Description Similar to H1: Homeobox protein SBH1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g62360`	Required for shoot apical meristem (SAM) formation during embryogenesis.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os07g0129700`	Probable transcription factor that may be involved in shoot formation during embryogenesis.	Isolation and characterization of a rice homebox gene, OSH15.1998 · DOI: 10.1023/a:1006065622251

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009990 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0009691 cytokinin biosynthetic process Biological Process

GO:0009888 tissue development Biological Process

GO:0009934 regulation of meristem structural organization Biological Process

GO:0010497 plasmodesmata-mediated intercellular transport Biological Process

GO:0010582 floral meristem determinacy Biological Process

GO:0019827 stem cell population maintenance Biological Process

GO:0048440 carpel development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005768 endosome Cellular Component

KEGG gene cross-reference

ath:AT1G62360

dosa:Os07g0129700

gmx:547796

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.978

Rank 1 · LXL04_009990 · OH-1004

Cytoplasm0.087

Rank 2 · LXL04_009990 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_009990 · OH-1004

Endoplasmic reticulum0.014

Rank 4 · LXL04_009990 · OH-1004

Plastid0.010

Rank 5 · LXL04_009990 · 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.

PF03790.19KNOX1101-140 aa

PF03791.19KNOX2170-215 aa

PF03789.19ELK268-289 aa

PF05920.18Homeobox_KN308-347 aa

PF00046.36Homeodomain315-348 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009990	`PF03790.19`	KNOX1	101	140	4e-22	78.4
LXL04_009990	`PF03791.19`	KNOX2	170	215	6.5e-22	77.5
LXL04_009990	`PF03789.19`	ELK	268	289	2.6e-11	43.8
LXL04_009990	`PF05920.18`	Homeobox_KN	308	347	1.1e-18	67.5
LXL04_009990	`PF00046.36`	Homeodomain	315	348	6.7e-07	29.8

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
`Q38874`	Arabidopsis thaliana	Homeobox protein SHOOT MERISTEMLESS	70.671%	Swiss-Prot	strong database homology
`O80416`	Oryza sativa subsp. japonica	Homeobox protein knotted-1-like 12	53.846%	Swiss-Prot	strong database homology

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