LXL04_001539 | RubberDandelionOmics

Gene overview

LXL04_001539

Reference: OH-1004 Chr: Chr01 Coordinates: 28648574-28650315 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1296 bp · LXL04_001539|LXL04_001539|OH1004|cDNA

ATGAAAGAACACATCCTTTTGGATTTGAATGAGGAGTCTGTTGAAGAAAACTCAATGAATGCTCAACATGAAAACAATGCTATTGAAGAACAAAGTCAAAACAACATTGCAAATTTTGAAGAACCGTTCGTTGtttatgcGAGAAAGAATGGGTTTTCCGTTCGAAAAGGAAGGTTTGTGAACAAAAAAACCGGAGAAAAGAAAATACGTGACTTTTTTTGTCATCGTGAAGGAAAATCGGAGTTAAAAAAGGATTACAC...

CDS

Download CDS FASTA

1296 bp · LXL04_001539|LXL04_001539|OH1004|CDS

ATGAAAGAACACATCCTTTTGGATTTGAATGAGGAGTCTGTTGAAGAAAACTCAATGAATGCTCAACATGAAAACAATGCTATTGAAGAACAAAGTCAAAACAACATTGCAAATTTTGAAGAACCGTTCGTTGTTTATGCGAGAAAGAATGGGTTTTCCGTTCGAAAAGGAAGGTTTGTGAACAAAAAAACCGGAGAAAAGAAAATACGTGACTTTTTTTGTCATCGTGAAGGAAAATCGGAGTTAAAAAAGGATTACAC...

Protein

Download Protein FASTA

431 aa · LXL04_001539|LXL04_001539|OH1004|PROTEIN

MKEHILLDLNEESVEENSMNAQHENNAIEEQSQNNIANFEEPFVVYARKNGFSVRKGRFVNKKTGEKKIRDFFCHREGKSELKKDYTKVPRNRGYTRCECKAHMHITLRRINEIFPEEWQVTKFVTEHNHTLLSTQEVRFLPSYRNITLEDEKRILLLKEGGLSVTQIMRVMELERNVRHGELSFLKKDVHNLFTKNHKLQSENDAKEILEYCQSAKNSENRLEHIFWCPAHCFELYQKYGDVVVFDTTYKVDLAIEDVG...

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_001539`
TK1151 ID	TkA06G101580
OH-1004 ID	LXL04_001539
Relationship / confidence	Multi Candidate From Tk1151 / Complex relationship
Protein identity (%)	69.700
Protein coverage (%)	TK1151 76.214 / OH-1004 60.325 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_001539

Location Chr01:28648574-28650315 (-)

Description Similar to FRS11: Protein FAR1-RELATED SEQUENCE 11

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g10240`	Putative transcription activator involved in regulating light control of development.	No verified direct reference in this release
`At5g28530`	Putative protein FAR1-RELATED SEQUENCE 10.	No verified direct reference in this release
`At4g38180`	Putative transcription activator involved in regulating light control of development.	No verified direct reference in this release
`At4g38170`	Putative transcription activator involved in regulating light control of development.	Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development.2004 · DOI: 10.1104/pp.104.052191
`At4g19990`	Putative transcription activator involved in regulating light control of development.	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_001539 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0005634 nucleus Cellular Component

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G10240

ath:AT4G38180

ath:AT5G28530

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.

Nucleus0.940

Rank 1 · LXL04_001539 · OH-1004

Cytoplasm0.134

Rank 2 · LXL04_001539 · OH-1004

Mitochondrion0.023

Rank 3 · LXL04_001539 · OH-1004

Cell membrane0.017

Rank 4 · LXL04_001539 · OH-1004

Endoplasmic reticulum0.010

Rank 5 · LXL04_001539 · 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.

PF03101.22FAR145-133 aa

PF26175.1HTH_FAR1146-200 aa

PF04434.23SWIM330-364 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001539	`PF03101.22`	FAR1	45	133	7.1e-18	65.8
LXL04_001539	`PF26175.1`	HTH_FAR1	146	200	2e-23	82.6
LXL04_001539	`PF04434.23`	SWIM	330	364	7.1e-08	32.5

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
`Q9SY66`	Arabidopsis thaliana	Protein FAR1-RELATED SEQUENCE 11	37.121%	Swiss-Prot	moderate database homology
`Q9LKR4`	Arabidopsis thaliana	Putative protein FAR1-RELATED SEQUENCE 10	32.967%	Swiss-Prot	moderate database homology
`Q9SZL8`	Arabidopsis thaliana	Protein FAR1-RELATED SEQUENCE 5	28.000%	Swiss-Prot	weak database homology
`Q9SZL7`	Arabidopsis thaliana	Protein FAR1-RELATED SEQUENCE 9	30.827%	Swiss-Prot	weak database homology
`Q5UBY2`	Arabidopsis thaliana	Protein FAR1-RELATED SEQUENCE 1	35.593%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card