LXL04_032998 | RubberDandelionOmics

Gene overview

LXL04_032998

Reference: OH-1004 Chr: Chr07 Coordinates: 33064444-33066066 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

996 bp · LXL04_032998|LXL04_032998|OH1004|cDNA

ATGGATGAGAGAGCAGACTCGTCGGAGAACCCAATGGGACATTTCAACGGCGGCAGCTTCAACATGTTCCAAGTCGATTTTATGCAAGAAACCGGATTCGAAAATTTCATTTCTGGATTCAGAGGCGAGATGGCGGATCCCATCGGGAAATTCTGCTTAGACTACGACTGCAATCACCTTACCGACGCCTGCACGGATCTTCAGCTGCTGCCGCTGCCGTACGTTCACAATGAAGCAATCGttactggtggtggtggtgg...

CDS

Download CDS FASTA

996 bp · LXL04_032998|LXL04_032998|OH1004|CDS

ATGGATGAGAGAGCAGACTCGTCGGAGAACCCAATGGGACATTTCAACGGCGGCAGCTTCAACATGTTCCAAGTCGATTTTATGCAAGAAACCGGATTCGAAAATTTCATTTCTGGATTCAGAGGCGAGATGGCGGATCCCATCGGGAAATTCTGCTTAGACTACGACTGCAATCACCTTACCGACGCCTGCACGGATCTTCAGCTGCTGCCGCTGCCGTACGTTCACAATGAAGCAATCGTTACTGGTGGTGGTGGTGG...

Protein

Download Protein FASTA

331 aa · LXL04_032998|LXL04_032998|OH1004|PROTEIN

MDERADSSENPMGHFNGGSFNMFQVDFMQETGFENFISGFRGEMADPIGKFCLDYDCNHLTDACTDLQLLPLPYVHNEAIVTGGGGGGGVDTGIGGYDAMGLHSNLIWNHESEDVVFGDDNSSETATTGNPDTPTPRSGGGGGPKGDRSRTLISERKRRSGMKEKLYALRSLVPNITKMDKASIVGDAAKYIQDLQTQARNLKAEIETIEALENHKTSPQNTKKIRATNAFPIQKKISKMDVFQVEEKGYYVRLVCNKGR...

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_032998`
TK1151 ID	TkA08G219320
OH-1004 ID	LXL04_032998
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.200
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_032998

Location Chr07:33064444-33066066 (-)

Description Similar to FIT: Transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g28160`	Transcription factor.	The essential basic helix-loop-helix protein FIT1 is required for the iron deficiency response.2004 · DOI: 10.1105/tpc.104.024315 AtbHLH29 of Arabidopsis thaliana is a functional ortholog of tomato FER involved in controlling iron acquisition in strategy I plants.2005 · DOI: 10.1038/sj.cr.7290331
`At5g57150`	Transcription factor bHLH35.	No verified direct reference in this release
`At4g29930`	Transcription factor bHLH27.	No verified direct reference in this release
`At2g16910`	Transcription factor.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0381700`	Transcription factor involved in positive regulation of genes involved in strategy II iron acquisition, including genes for mugineic acid (MA) family phytosiderophores biosynthesis, and genes involved in S-adenosylmethionine cycle and iron transport.	A transcription factor OsbHLH156 regulates Strategy II iron acquisition through localising IRO2 to the nucleus in rice.2020 · DOI: 10.1111/nph.16232

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032998 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009555 pollen development Biological Process

GO:0010039 response to iron ion Biological Process

GO:0034756 regulation of iron ion transport Biological Process

GO:0048658 anther wall tapetum development Biological Process

GO:0005634 nucleus Cellular Component

GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding Molecular Function

GO:0003682 chromatin binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

GO:0043565 sequence-specific DNA binding Molecular Function

GO:0046983 protein dimerization activity Molecular Function

KEGG gene cross-reference

ath:AT2G16910

ath:AT2G28160

ath:AT4G29930

ath:AT5G57150

osa:107276663

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.

Nucleus0.965

Rank 1 · LXL04_032998 · OH-1004

Cytoplasm0.102

Rank 2 · LXL04_032998 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_032998 · OH-1004

Endoplasmic reticulum0.020

Rank 4 · LXL04_032998 · OH-1004

Plastid0.011

Rank 5 · LXL04_032998 · 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.

PF00010.32HLH151-196 aa

PF23177.2bHLH_IRO3154-213 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032998	`PF00010.32`	HLH	151	196	1.3e-10	41.7
LXL04_032998	`PF23177.2`	bHLH_IRO3	154	213	2.5e-06	28.5

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
`Q0V7X4`	Arabidopsis thaliana	Transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR	45.833%	Swiss-Prot	moderate database homology
`Q2HIV9`	Arabidopsis thaliana	Transcription factor bHLH35	33.898%	Swiss-Prot	weak database homology
`Q700E3`	Arabidopsis thaliana	Transcription factor bHLH27	30.542%	Swiss-Prot	moderate database homology
`Q9ZVX2`	Arabidopsis thaliana	Transcription factor ABORTED MICROSPORES	30.263%	Swiss-Prot	weak database homology
`A0A0N7KIY3`	Oryza sativa subsp. japonica	Transcription factor BHLH156	33.953%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card