LXL04_012689 | RubberDandelionOmics

Gene overview

LXL04_012689

Reference: OH-1004 Chr: Chr03 Coordinates: 16966420-16969037 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2184 bp · LXL04_012689|LXL04_012689|OH1004|cDNA

ATGGCTTCTCTCTGTATCCCTCTATCAAAACCACAACTCCTAAAACACTGCTTCTTCCATAAACTCTCAAAAATATCCAAACCCCTTCATCGTTTCTATTCATCTGCCGATAAACCACAAGTTGAAGAAAATCCAGACCCGAAATCACACCTTTCGACATTTGGATCACAAGCCGGGACGATCGAAAATGGAAAATTTCAATTCCGAGGTGAGCATAATCCCAATCTAGAGAACCTTGAAGATGCTGAGGGATCCGGGTT...

CDS

Download CDS FASTA

2184 bp · LXL04_012689|LXL04_012689|OH1004|CDS

ATGGCTTCTCTCTGTATCCCTCTATCAAAACCACAACTCCTAAAACACTGCTTCTTCCATAAACTCTCAAAAATATCCAAACCCCTTCATCGTTTCTATTCATCTGCCGATAAACCACAAGTTGAAGAAAATCCAGACCCGAAATCACACCTTTCGACATTTGGATCACAAGCCGGGACGATCGAAAATGGAAAATTTCAATTCCGAGGTGAGCATAATCCCAATCTAGAGAACCTTGAAGATGCTGAGGGATCCGGGTT...

Protein

Download Protein FASTA

727 aa · LXL04_012689|LXL04_012689|OH1004|PROTEIN

MASLCIPLSKPQLLKHCFFHKLSKISKPLHRFYSSADKPQVEENPDPKSHLSTFGSQAGTIENGKFQFRGEHNPNLENLEDAEGSGFKHDRETYYEMIEILCKNRKLEDAKRILLGMSKNGVDYDEDLFVLLINGYAKMNRKWDIVKNCLKIFSKMEELGVPRTIKSYNPMLEVILSEKKYTMAEKFFHKMLSEGVVPTKQTYTLMITGLCRSSSIETANRFFQDMKSQNHLPDSALYNTMINGYVQVKKMEEAEKLLME...

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_012689`
TK1151 ID	TkA02G545400
OH-1004 ID	LXL04_012689
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.800
Protein coverage (%)	TK1151 95.238 / OH-1004 57.772 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_012689

Location Chr03:16966420-16969037 (-)

Description Similar to 29 kDa ribonucleoprotein B, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g37220`	Could be involved in splicing and/or processing of chloroplast RNA's.	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_012689 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0009409 response to cold Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0045087 innate immune response Biological Process

GO:1901259 chloroplast rRNA processing Biological Process

GO:0005783 endoplasmic reticulum Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009534 chloroplast thylakoid Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0009579 thylakoid Cellular Component

GO:0009941 chloroplast envelope Cellular Component

KEGG gene cross-reference

ath:AT2G37220

nsy:104230409

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.

Plastid0.572

Rank 1 · LXL04_012689 · OH-1004

Mitochondrion0.363

Rank 2 · LXL04_012689 · OH-1004

Nucleus0.054

Rank 3 · LXL04_012689 · OH-1004

Cytoplasm0.031

Rank 4 · LXL04_012689 · OH-1004

Cell membrane0.010

Rank 5 · LXL04_012689 · 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.

PF29070.1MSC6_N88-224 aa

PF13041.13PPR_293-138 aa

PF13812.13PPR_3151-207 aa

PF23276.3TPR_24156-257 aa

PF13041.13PPR_2165-212 aa

PF29070.1MSC6_N179-258 aa

PF12854.14PPR_1195-227 aa

PF01535.27PPR202-230 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012689	`PF29070.1`	MSC6_N	88	224	1.5e-15	57.9
LXL04_012689	`PF13041.13`	PPR_2	93	138	3.8e-58	194.1
LXL04_012689	`PF13812.13`	PPR_3	151	207	1.1e-36	125.4
LXL04_012689	`PF23276.3`	TPR_24	156	257	8.5e-12	45.8
LXL04_012689	`PF13041.13`	PPR_2	165	212	3.8e-58	194.1
LXL04_012689	`PF29070.1`	MSC6_N	179	258	1.5e-15	57.9
LXL04_012689	`PF12854.14`	PPR_1	195	227	1.7e-40	137.2
LXL04_012689	`PF01535.27`	PPR	202	230	2.9e-42	140.7
LXL04_012689	`PF17177.11`	PPR_long	214	288	1.4e-18	67.8
LXL04_012689	`PF29070.1`	MSC6_N	214	363	1.5e-15	57.9
LXL04_012689	`PF13812.13`	PPR_3	222	280	1.1e-36	125.4
LXL04_012689	`PF12854.14`	PPR_1	230	262	1.7e-40	137.2
LXL04_012689	`PF13041.13`	PPR_2	233	282	3.8e-58	194.1
LXL04_012689	`PF01535.27`	PPR	238	265	2.9e-42	140.7
LXL04_012689	`PF12854.14`	PPR_1	266	297	1.7e-40	137.2
LXL04_012689	`PF01535.27`	PPR	271	300	2.9e-42	140.7

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
`Q9ZUU4`	Arabidopsis thaliana	RNA-binding protein CP29B, chloroplastic	62.174%	Swiss-Prot	weak database homology

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