LXL04_027033 | RubberDandelionOmics

Gene overview

LXL04_027033

Reference: OH-1004 Chr: Chr06 Coordinates: 7474625-7477378 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1131 bp · LXL04_027033|LXL04_027033|OH1004|cDNA

atggAGGGAGATGGTGGAGGAGGGAGTTCATCATGTTTGATGAGTTTTGGAGACAACAACATCATTAGTAGCAGCAGCAATAGTAATAATACCAACGTTGGAGCACTGTGTCTTCCTCCGCCTCCTGTTGCATATaacaccaacaccaacaacaaTAACCTAGTTTTCACCTCTCAAGATCACCATCATCACCATAGTACCTGCGGCACTTCCAATTCTGCCATGATGCTTGAAAACAACACCATTAATGGCGGAGGGCT...

CDS

Download CDS FASTA

1131 bp · LXL04_027033|LXL04_027033|OH1004|CDS

ATGGAGGGAGATGGTGGAGGAGGGAGTTCATCATGTTTGATGAGTTTTGGAGACAACAACATCATTAGTAGCAGCAGCAATAGTAATAATACCAACGTTGGAGCACTGTGTCTTCCTCCGCCTCCTGTTGCATATAACACCAACACCAACAACAATAACCTAGTTTTCACCTCTCAAGATCACCATCATCACCATAGTACCTGCGGCACTTCCAATTCTGCCATGATGCTTGAAAACAACACCATTAATGGCGGAGGGCT...

Protein

Download Protein FASTA

376 aa · LXL04_027033|LXL04_027033|OH1004|PROTEIN

MEGDGGGGSSSCLMSFGDNNIISSSSNSNNTNVGALCLPPPPVAYNTNTNNNNLVFTSQDHHHHHSTCGTSNSAMMLENNTINGGGLTFMTSSSCSSSLKAKIMSHPHYPRLLSAYLNCQKIGAPPEVVERLEEACRASVVQAAMSSRSGSAGCETGTSDGGGGGGGGGMNMMIIGQDPALDQFMEAYCEMLIKYEQELSKPFKEAMLFLSRVESQFKAISISTSDSADGEGGMDKNGSSEEELDVNNNLVDPQAEDQEL...

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_027033`
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_027033

Location Chr06:7474625-7477378 (+)

Description Similar to STM: Homeobox protein SHOOT MERISTEMLESS

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
`At4g08150`	May play a role in meristem function, and may be involved in maintaining cells in an undifferentiated, meristematic state, and its expression disappears at the same time the shoot apex undergoes the transition from vegetative to reproductive development.	ASYMMETRIC LEAVES1 reveals knox gene redundancy in Arabidopsis.2002 · DOI: 10.1242/dev.129.8.1957 Developmental regulation and significance of KNOX protein trafficking in Arabidopsis.2003 · DOI: 10.1242/dev.00618 A knotted1-like homeobox gene in Arabidopsis is expressed in the vegetative meristem and dramatically alters leaf morphology when overexpressed in transgenic plants.1994 · DOI: 10.1105/tpc.6.12.1859

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_027033 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0001708 cell fate specification 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:0010051 xylem and phloem pattern formation Biological Process

GO:0010089 xylem development 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:0045165 cell fate commitment Biological Process

GO:0048440 carpel development Biological Process

KEGG gene cross-reference

ath:AT1G62360

ath:AT4G08150

dosa:Os07g0129700

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.

Nucleus0.979

Rank 1 · LXL04_027033 · OH-1004

Cytoplasm0.081

Rank 2 · LXL04_027033 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_027033 · OH-1004

Endoplasmic reticulum0.015

Rank 4 · LXL04_027033 · OH-1004

Plastid0.010

Rank 5 · LXL04_027033 · 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.

PF03790.19KNOX199-138 aa

PF03791.19KNOX2175-220 aa

PF03789.19ELK259-280 aa

PF05920.18Homeobox_KN299-338 aa

PF00046.36Homeodomain306-339 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027033	`PF03790.19`	KNOX1	99	138	1.4e-22	79.9
LXL04_027033	`PF03791.19`	KNOX2	175	220	1.9e-21	76.0
LXL04_027033	`PF03789.19`	ELK	259	280	2.6e-11	43.8
LXL04_027033	`PF05920.18`	Homeobox_KN	299	338	4.2e-19	68.8
LXL04_027033	`PF00046.36`	Homeodomain	306	339	6.3e-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	70.724%	Swiss-Prot	strong database homology
`P46639`	Arabidopsis thaliana	Homeobox protein knotted-1-like 1	55.957%	Swiss-Prot	strong database homology
`O80416`	Oryza sativa subsp. japonica	Homeobox protein knotted-1-like 12	54.122%	Swiss-Prot	strong database homology

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