LXL04_004252 | RubberDandelionOmics

Gene overview

LXL04_004252

Reference: OH-1004 Chr: Chr01 Coordinates: 131143055-131145498 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1365 bp · LXL04_004252|LXL04_004252|OH1004|cDNA

ATGCTAAGCAAGCTCTACTCAAATCGTTGCTTCTGTACTGCAATTCAATCACCACGTCCATGGTTATTCGTCGGTTTGGGCAATCCCGGTGACAAATTCAAAGGAACAAGACACAATTTTTCTGCAAATCCATTTTCGGAAAAGGCTTGTCAGCTTCTCTCAGATTCTAATTTCTTTTTTCTTCACTTTCAAAATCGAATCCATGATTTGGGAAAACTAATGAAGAATTCCATTGTTGACGTATCAGGAATTGTTGATGG...

CDS

Download CDS FASTA

1365 bp · LXL04_004252|LXL04_004252|OH1004|CDS

ATGCTAAGCAAGCTCTACTCAAATCGTTGCTTCTGTACTGCAATTCAATCACCACGTCCATGGTTATTCGTCGGTTTGGGCAATCCCGGTGACAAATTCAAAGGAACAAGACACAATTTTTCTGCAAATCCATTTTCGGAAAAGGCTTGTCAGCTTCTCTCAGATTCTAATTTCTTTTTTCTTCACTTTCAAAATCGAATCCATGATTTGGGAAAACTAATGAAGAATTCCATTGTTGACGTATCAGGAATTGTTGATGG...

Protein

Download Protein FASTA

454 aa · LXL04_004252|LXL04_004252|OH1004|PROTEIN

MLSKLYSNRCFCTAIQSPRPWLFVGLGNPGDKFKGTRHNFSANPFSEKACQLLSDSNFFFLHFQNRIHDLGKLMKNSIVDVSGIVDGVPVLLAKPQTYMNLSGESSGPLAAYYKLPLNRVVVFHDDMDLPCGVLRLQPKGGHGSHNGMKSVIYHFRGNREFARLRIGIGKPPGQMDPKAFLLQKFNATAQQRIDVGLKEGVDALKKLVTKGVEEAGRGFNTDQKYKHIKIADIIMAKHLCNFELVNMGKMVEGGMKKGPW...

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_004252`
TK1151 ID	TkA01G189760
OH-1004 ID	LXL04_004252
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	79.200
Protein coverage (%)	TK1151 89.928 / OH-1004 27.533 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_004252

Location Chr01:131143055-131145498 (+)

Description Similar to At5g19830: Peptidyl-tRNA hydrolase, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g19830`	The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.	No verified direct reference in this release
`At3g13540`	Transcription activator, when associated with BHLH002/EGL3/MYC146, BHLH012/MYC1 or BHLH042/TT8.	No verified direct reference in this release
`At5g16140`	Required for the splicing of group IIB introns in chloroplasts.	No verified direct reference in this release
`At5g38290`	Required for the splicing of group IIB introns in chloroplasts.	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_004252 · 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:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0010090 trichome morphogenesis Biological Process

GO:0010214 seed coat development Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0030154 cell differentiation Biological Process

GO:0048354 mucilage biosynthetic process involved in seed coat development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

KEGG gene cross-reference

ath:AT3G13540

ath:AT5G16140

ath:AT5G19830

ath:AT5G38290

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.

Mitochondrion0.340

Rank 1 · LXL04_004252 · OH-1004

Nucleus0.255

Rank 2 · LXL04_004252 · OH-1004

Plastid0.231

Rank 3 · LXL04_004252 · OH-1004

Cytoplasm0.154

Rank 4 · LXL04_004252 · OH-1004

Peroxisome0.033

Rank 5 · LXL04_004252 · 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.

PF01195.27Pept_tRNA_hydro22-223 aa

PF00249.38Myb_DNA-binding257-304 aa

PF13921.13Myb_DNA-bind_6260-318 aa

PF00249.38Myb_DNA-binding311-355 aa

PF13921.13Myb_DNA-bind_6314-361 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004252	`PF01195.27`	Pept_tRNA_hydro	22	223	1.5e-53	182.1
LXL04_004252	`PF00249.38`	Myb_DNA-binding	257	304	1.7e-34	118.4
LXL04_004252	`PF13921.13`	Myb_DNA-bind_6	260	318	9.4e-19	68.1
LXL04_004252	`PF00249.38`	Myb_DNA-binding	311	355	1.7e-34	118.4
LXL04_004252	`PF13921.13`	Myb_DNA-bind_6	314	361	9.4e-19	68.1

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q6NLS8`	Arabidopsis thaliana	Peptidyl-tRNA hydrolase, mitochondrial	61.506%	Swiss-Prot	moderate database homology
`Q38850`	Arabidopsis thaliana	Transcription repressor MYB5	59.804%	Swiss-Prot	weak database homology
`Q9LF14`	Arabidopsis thaliana	Chloroplastic group IIB intron splicing facilitator CRS2-B, chloroplastic	48.341%	Swiss-Prot	weak database homology
`Q9FKN4`	Arabidopsis thaliana	Chloroplastic group IIB intron splicing facilitator CRS2-A, chloroplastic	48.357%	Swiss-Prot	weak database homology

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