LXL04_029359 | RubberDandelionOmics

Gene overview

LXL04_029359

Reference: OH-1004 Chr: Chr06 Coordinates: 88353447-88355852 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1188 bp · LXL04_029359|LXL04_029359|OH1004|cDNA

ATGGACTCGCGAGAGTCATTAGCACCACCACCGTCGCTCCAACGACATCCAATTCACCACCAACGGCCGCTACCACAGACGATGATGCCGCCAAATTCATACAATACCCACCACCACCACTTACCTAACAACTCCAACAGTGCTCCGGCGAACAACAACAGTATCATAAGTTCCGATTCGCTGCAACAACGTTTCGCCTTTGATGGACCTGACCAGTATGGAGACGGATCGTCTCCTCCTGGCGGCTTTAGGGCTGGTGG...

CDS

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1188 bp · LXL04_029359|LXL04_029359|OH1004|CDS

ATGGACTCGCGAGAGTCATTAGCACCACCACCGTCGCTCCAACGACATCCAATTCACCACCAACGGCCGCTACCACAGACGATGATGCCGCCAAATTCATACAATACCCACCACCACCACTTACCTAACAACTCCAACAGTGCTCCGGCGAACAACAACAGTATCATAAGTTCCGATTCGCTGCAACAACGTTTCGCCTTTGATGGACCTGACCAGTATGGAGACGGATCGTCTCCTCCTGGCGGCTTTAGGGCTGGTGG...

Protein

Download Protein FASTA

395 aa · LXL04_029359|LXL04_029359|OH1004|PROTEIN

MDSRESLAPPPSLQRHPIHHQRPLPQTMMPPNSYNTHHHHLPNNSNSAPANNNSIISSDSLQQRFAFDGPDQYGDGSSPPGGFRAGGFSIEPARKKRGRPRKYSPSPDGNIALALAPAPITTGATAAGGGGQLESSNDGGSAGATGTPNTDPSAKKHRGRPPGSGKKQLDALGAPGVGFTPHVITVKAGEDIASKITAFSQQGPRTVCILSANGAISNVTLRQPAMSGGSVTYEGRFEIISLSGSFLLADSNGNNQSNKS...

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_029359`
TK1151 ID	TkA07G306810
OH-1004 ID	LXL04_029359
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_029359

Location Chr06:88353447-88355852 (+)

Description Similar to AHL13: AT-hook motif nuclear-localized protein 13

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g17950`	Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).	No verified direct reference in this release
`At2g33620`	Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).	No verified direct reference in this release
`At5g46640`	Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).	No verified direct reference in this release
`At4g12080`	Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).	Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces.2004 · DOI: 10.1007/s11103-004-3249-5
`At4g25320`	Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) (By similarity).	Cell-to-cell movement of two interacting AT-hook factors in Arabidopsis root vascular tissue patterning.2013 · DOI: 10.1105/tpc.112.102210

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029359 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0010051 xylem and phloem pattern formation Biological Process

GO:0010089 xylem development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0098687 chromosomal region Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003680 minor groove of adenine-thymine-rich DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

ath:AT2G33620

ath:AT4G12080

ath:AT4G17950

ath:AT4G25320

ath:AT5G46640

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.

Nucleus0.980

Rank 1 · LXL04_029359 · OH-1004

Cytoplasm0.072

Rank 2 · LXL04_029359 · OH-1004

Cell membrane0.025

Rank 3 · LXL04_029359 · OH-1004

Endoplasmic reticulum0.017

Rank 4 · LXL04_029359 · OH-1004

Plastid0.010

Rank 5 · LXL04_029359 · 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.

PF03479.22PCC176-296 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029359	`PF03479.22`	PCC	176	296	3.2e-37	128.0

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
`Q940I0`	Arabidopsis thaliana	AT-hook motif nuclear-localized protein 13	56.202%	Swiss-Prot	moderate database homology
`O22812`	Arabidopsis thaliana	AT-hook motif nuclear-localized protein 10	50.502%	Swiss-Prot	strong database homology
`Q9FIR1`	Arabidopsis thaliana	AT-hook motif nuclear-localized protein 8	58.333%	Swiss-Prot	moderate database homology
`Q8VYJ2`	Arabidopsis thaliana	AT-hook motif nuclear-localized protein 1	50.667%	Swiss-Prot	moderate database homology
`Q9SB31`	Arabidopsis thaliana	AT-hook motif nuclear-localized protein 3	42.857%	Swiss-Prot	moderate database homology

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