LXL04_028313 | RubberDandelionOmics

Gene overview

LXL04_028313

Reference: OH-1004 Chr: Chr06 Coordinates: 37355506-37361514 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2649 bp · LXL04_028313|LXL04_028313|OH1004|cDNA

ATGGCAATGGCTGCTTTCAGTGGTATATCACATTGCCATCACAGGCTCTGGTGGCAACCCAACACGTCAAAACTTCCTGTTTCTTGCTCTATGCCTCCTCCTACATTCACAGGTACAAGTCATGGATCTAAAACGGGACCTAGACGTTCCGGAAGATTTGAAGGGGCTGGAAAGAGCATGGAAGATTCCGTGAAGCGCAAAATGGAGAAATTTTATGAAGGGTCAAACGGTCCACCTCTTCGTGTTCTTCCAATTGGTGG...

CDS

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2649 bp · LXL04_028313|LXL04_028313|OH1004|CDS

ATGGCAATGGCTGCTTTCAGTGGTATATCACATTGCCATCACAGGCTCTGGTGGCAACCCAACACGTCAAAACTTCCTGTTTCTTGCTCTATGCCTCCTCCTACATTCACAGGTACAAGTCATGGATCTAAAACGGGACCTAGACGTTCCGGAAGATTTGAAGGGGCTGGAAAGAGCATGGAAGATTCCGTGAAGCGCAAAATGGAGAAATTTTATGAAGGGTCAAACGGTCCACCTCTTCGTGTTCTTCCAATTGGTGG...

Protein

Download Protein FASTA

882 aa · LXL04_028313|LXL04_028313|OH1004|PROTEIN

MAMAAFSGISHCHHRLWWQPNTSKLPVSCSMPPPTFTGTSHGSKTGPRRSGRFEGAGKSMEDSVKRKMEKFYEGSNGPPLRVLPIGGLGEIGMNCMLVGNFDRYILIDAGVMFPDYEDLGVQKIIPDTTFIKKWSHKIEAVVITHGHEDHIGALPWVIPALDSRTPIFASTFTMELIKKRLKESGIFVPSRLKAFKTKRRFQAGPFEIEPIRVTHSIPDCSGLVLRCSDGVILHTGDWKIDESPLDGQVFDREGLEQLSK...

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_028313`
TK1151 ID	TkA07G141670
OH-1004 ID	LXL04_028313
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.800
Protein coverage (%)	TK1151 99.756 / OH-1004 93.537 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

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Basic Information and Functional Annotation

Gene ID LXL04_028313

Location Chr06:37355506-37361514 (+)

Description Similar to RNJ: Ribonuclease J

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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_028313 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009536 plastid Cellular Component

KEGG gene cross-reference

ath:AT5G63420

cgb:cg2160

cgl:Cgl1970

msb:LJ00_13360

msg:MSMEI_2620

msm:MSMEG_2685

smel:SM2011_c01929

tth:TT_C0775

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.

Plastid0.803

Rank 1 · LXL04_028313 · OH-1004

Mitochondrion0.106

Rank 2 · LXL04_028313 · OH-1004

Nucleus0.087

Rank 3 · LXL04_028313 · OH-1004

Cytoplasm0.029

Rank 4 · LXL04_028313 · OH-1004

Cell membrane0.023

Rank 5 · LXL04_028313 · 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.

PF00753.34Lactamase_B94-237 aa

PF12706.14Lactamase_B_2103-239 aa

PF22505.2RNase_J_b_CASP297-422 aa

PF07521.18RMMBL431-483 aa

PF17770.8RNase_J_C534-642 aa

PF13837.13Myb_DNA-bind_4733-817 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028313	`PF00753.34`	Lactamase_B	94	237	2.5e-07	31.6
LXL04_028313	`PF12706.14`	Lactamase_B_2	103	239	1.9e-09	38.1
LXL04_028313	`PF22505.2`	RNase_J_b_CASP	297	422	7.1e-29	100.8
LXL04_028313	`PF07521.18`	RMMBL	431	483	6.1e-09	36.5
LXL04_028313	`PF17770.8`	RNase_J_C	534	642	4e-25	89.5
LXL04_028313	`PF13837.13`	Myb_DNA-bind_4	733	817	3.5e-22	79.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q84W56`	Arabidopsis thaliana	Ribonuclease J	67.565%	Swiss-Prot	strong database homology

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