LXL04_029140 | RubberDandelionOmics

Gene overview

LXL04_029140

Reference: OH-1004 Chr: Chr06 Coordinates: 81770534-81771550 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

864 bp · LXL04_029140|LXL04_029140|OH1004|cDNA

ATGTATGGTGGAGGCAGCACCGGTGGCCGTGGTGGAGGAAGCGATAACAATGAAGCCCTAAATCAACTGACACAGATGATGATGATTGCTCCGACGCCTCCCCCAGTGATGGTGGTTGGTGCGGAGGAGTTTTCGAGAAGGGACGAGAGGGTACCGATGTGGAGCCAACAGGAGACGAGGGATTTCATTGCGATTCGTGGGGAGTTGGAGAGGGATTTCACCATGGCGAAGCGGAACAAGAGTCTTTGGGAGGTTGTGGC...

CDS

Download CDS FASTA

864 bp · LXL04_029140|LXL04_029140|OH1004|CDS

ATGTATGGTGGAGGCAGCACCGGTGGCCGTGGTGGAGGAAGCGATAACAATGAAGCCCTAAATCAACTGACACAGATGATGATGATTGCTCCGACGCCTCCCCCAGTGATGGTGGTTGGTGCGGAGGAGTTTTCGAGAAGGGACGAGAGGGTACCGATGTGGAGCCAACAGGAGACGAGGGATTTCATTGCGATTCGTGGGGAGTTGGAGAGGGATTTCACCATGGCGAAGCGGAACAAGAGTCTTTGGGAGGTTGTGGC...

Protein

Download Protein FASTA

287 aa · LXL04_029140|LXL04_029140|OH1004|PROTEIN

MYGGGSTGGRGGGSDNNEALNQLTQMMMIAPTPPPVMVVGAEEFSRRDERVPMWSQQETRDFIAIRGELERDFTMAKRNKSLWEVVAAKMKEIGYTRTPDQCKCKWKNLINRYKGKETSDRDNTRSFPFFDDLHALFTPQTPFESKKRVTRIDSYQSLQEISEDEDEDEDDENKITIPPRKKPEREKRSRPPTPKSSDPIREILHDFFQQQKMIDMQWRELMEKHAYERQLFEQEWRQSMERLEIERLKVEKLWREKEEQ...

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_029140`
TK1151 ID	TkA07G278940
OH-1004 ID	LXL04_029140
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 87.108 / OH-1004 87.108 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_029140

Location Chr06:81770534-81771550 (+)

Description Similar to GT-3B: Trihelix transcription factor GT-3b

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g38250`	Probable transcription factor that may play a role in the induction of CAM4 in response to pathogen and salt.	Pathogen- and NaCl-induced expression of the SCaM-4 promoter is mediated in part by a GT-1 box that interacts with a GT-1-like transcription factor.2004 · DOI: 10.1104/pp.104.041442
`At5g01380`	Probable transcription factor that binds specifically to the core DNA sequence 5'-GTTAC-3'.	Analysis of GT-3a identifies a distinct subgroup of trihelix DNA-binding transcription factors in Arabidopsis.2004 · DOI: 10.1016/s0014-5793(04)00222-4
`At1g13450`	Probable transcription factor that binds specifically to the core DNA sequence 5'-GGTTAA-3'.	No verified direct reference in this release
`At3g25990`	Probable transcription factor that binds specific DNA sequence.	No verified direct reference in this release
`At5g63420`	Essential protein required during embryogenesis, especially in initiating and maintaining the organization of shoot apical meristems (SAMs), cotyledons, and hypocotyls.	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_029140 · 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:0006364 rRNA processing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009942 longitudinal axis specification Biological Process

GO:0060918 auxin transport Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

KEGG gene cross-reference

ath:AT1G13450

ath:AT2G38250

ath:AT3G25990

ath:AT5G01380

ath:AT5G63420

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.

Nucleus0.981

Rank 1 · LXL04_029140 · OH-1004

Cytoplasm0.062

Rank 2 · LXL04_029140 · OH-1004

Cell membrane0.020

Rank 3 · LXL04_029140 · OH-1004

Endoplasmic reticulum0.012

Rank 4 · LXL04_029140 · OH-1004

Plastid0.009

Rank 5 · LXL04_029140 · 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.

PF13837.13Myb_DNA-bind_453-136 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029140	`PF13837.13`	Myb_DNA-bind_4	53	136	1.5e-22	80.5

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
`O80450`	Arabidopsis thaliana	Trihelix transcription factor GT-3b	41.833%	Swiss-Prot	moderate database homology
`Q9SDW0`	Arabidopsis thaliana	Trihelix transcription factor GT-3a	36.940%	Swiss-Prot	moderate database homology
`Q9FX53`	Arabidopsis thaliana	Trihelix transcription factor GT-1	40.000%	Swiss-Prot	weak database homology
`Q9LU92`	Arabidopsis thaliana	Trihelix transcription factor GT-4	40.909%	Swiss-Prot	weak database homology
`Q84W56`	Arabidopsis thaliana	Ribonuclease J	32.941%	Swiss-Prot	weak database homology

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