LXL04_039109 | RubberDandelionOmics

Gene overview

LXL04_039109

Reference: OH-1004 Chr: Chr09 Coordinates: 59441833-59443477 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

897 bp · LXL04_039109|LXL04_039109|OH1004|cDNA

ATGAAGAGAAACTTCAGTTGCTCTGATTCTTTGACTCATTTTCTCTCACACCCACTTGAAGGGGAGATAAAAGCAGAAGAAGACTGCATTTTCAACGGAGAATTTCAATCAATGGTAGACGGCCGTGGTGGCGGAGATGGAGAAGATTACGGTGGGGAAGAAACAGGGCAATTCGGTGACAAAAAGAGAAGATTAAGCAATCATCAAGTGAAATCATTAGAGAAAATATTTGAAGTCGATAACAAACTTGACCCAGAAAG...

CDS

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897 bp · LXL04_039109|LXL04_039109|OH1004|CDS

ATGAAGAGAAACTTCAGTTGCTCTGATTCTTTGACTCATTTTCTCTCACACCCACTTGAAGGGGAGATAAAAGCAGAAGAAGACTGCATTTTCAACGGAGAATTTCAATCAATGGTAGACGGCCGTGGTGGCGGAGATGGAGAAGATTACGGTGGGGAAGAAACAGGGCAATTCGGTGACAAAAAGAGAAGATTAAGCAATCATCAAGTGAAATCATTAGAGAAAATATTTGAAGTCGATAACAAACTTGACCCAGAAAG...

Protein

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298 aa · LXL04_039109|LXL04_039109|OH1004|PROTEIN

MKRNFSCSDSLTHFLSHPLEGEIKAEEDCIFNGEFQSMVDGRGGGDGEDYGGEETGQFGDKKRRLSNHQVKSLEKIFEVDNKLDPERKVKVAQDLGLQPRQVAIWFQNRRARWKTKQLERDYNLLKSSYDTLKHNYHKLEKEKEIIIKELVELKAKLHEETTQGSEEFEDRENVLFLGSDPTDTNHEVYTSLNYESTRKSLDLKDGFSDSDSSGVLNEENMNVSNDNGSSSLNMASFGLSSLCSSSATTSNHTGHVDPRT...

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_039109`
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_039109

Location Chr09:59441833-59443477 (-)

Description Similar to ATHB-16: Homeobox-leucine zipper protein ATHB-16

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g40060`	Probable transcription factor that may function as a negative regulator of the flowering time response to photoperiod.	No verified direct reference in this release
`At5g65310`	Probable transcription factor that acts as a positive regulator of ABA-responsiveness, mediating the inhibitory effect of ABA on growth during seedling establishment.	No verified direct reference in this release
`At2g22430`	Transcription activator that may act as growth regulators in response to water deficit.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0470500`	Probable transcription activator that binds to the DNA sequence 5'-CAAT[AT]ATTG-3'.	HD-Zip proteins of families I and II from rice: interactions and functional properties.2000 · DOI: 10.1007/pl00008671 Functional analysis of rice HOMEOBOX4 (Oshox4) gene reveals a negative function in gibberellin responses.2008 · DOI: 10.1007/s11103-007-9270-8
`UniProt: Q9XH37`	Probable transcription activator that binds to the DNA sequence 5'-CAAT[AT]ATTG-3'.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_039109 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009637 response to blue light Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009788 negative regulation of abscisic acid-activated signaling pathway Biological Process

GO:0030308 negative regulation of cell growth Biological Process

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

GO:0048510 regulation of timing of transition from vegetative to reproductive phase Biological Process

GO:0048573 photoperiodism, flowering Biological Process

GO:0048768 root hair cell tip growth Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT2G22430

ath:AT4G40060

ath:AT5G65310

dosa:Os09g0470500

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.

Nucleus0.978

Rank 1 · LXL04_039109 · OH-1004

Cytoplasm0.086

Rank 2 · LXL04_039109 · OH-1004

Cell membrane0.022

Rank 3 · LXL04_039109 · OH-1004

Endoplasmic reticulum0.012

Rank 4 · LXL04_039109 · OH-1004

Plastid0.010

Rank 5 · LXL04_039109 · 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.

PF00046.36Homeodomain61-114 aa

PF02183.24HALZ116-157 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039109	`PF00046.36`	Homeodomain	61	114	2.5e-17	63.1
LXL04_039109	`PF02183.24`	HALZ	116	157	1.4e-12	48.3

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
`Q940J1`	Arabidopsis thaliana	Homeobox-leucine zipper protein ATHB-16	37.143%	Swiss-Prot	moderate database homology
`P46667`	Arabidopsis thaliana	Homeobox-leucine zipper protein ATHB-5	50.000%	Swiss-Prot	moderate database homology
`P46668`	Arabidopsis thaliana	Homeobox-leucine zipper protein ATHB-6	49.367%	Swiss-Prot	moderate database homology
`Q6K498`	Oryza sativa subsp. japonica	Homeobox-leucine zipper protein HOX4	56.489%	Swiss-Prot	weak database homology
`Q9XH37`	Oryza sativa subsp. indica	Homeobox-leucine zipper protein HOX4	56.489%	Swiss-Prot	weak database homology

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