LXL04_024025 | RubberDandelionOmics

Gene overview

LXL04_024025

Reference: OH-1004 Chr: Chr05 Coordinates: 78138554-78142665 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2847 bp · LXL04_024025|LXL04_024025|OH1004|cDNA

ATGTTGCTTCAGCAACCTTCACCCTCTCCTAAAACCCTCCCAAACCCTTTTCTCTCCACACTAAATCTTCCTCAAAACCTTCTTCCCCAAATTCCTTTTCATTTTCGTCGCAATTCATTCAAACTTCACGCTTCCGCTTCCTCCGCCGATACGAAAAGTCTACCTCAATCCGCAATTCGAAGAATCGCCGATAAGCTTCGAAGTCTAGGTTACGTTGAAGACGATAGCATTAAGCAACAGCCTTCAGCACCAGAACAAAC...

CDS

Download CDS FASTA

2847 bp · LXL04_024025|LXL04_024025|OH1004|CDS

ATGTTGCTTCAGCAACCTTCACCCTCTCCTAAAACCCTCCCAAACCCTTTTCTCTCCACACTAAATCTTCCTCAAAACCTTCTTCCCCAAATTCCTTTTCATTTTCGTCGCAATTCATTCAAACTTCACGCTTCCGCTTCCTCCGCCGATACGAAAAGTCTACCTCAATCCGCAATTCGAAGAATCGCCGATAAGCTTCGAAGTCTAGGTTACGTTGAAGACGATAGCATTAAGCAACAGCCTTCAGCACCAGAACAAAC...

Protein

Download Protein FASTA

948 aa · LXL04_024025|LXL04_024025|OH1004|PROTEIN

MLLQQPSPSPKTLPNPFLSTLNLPQNLLPQIPFHFRRNSFKLHASASSADTKSLPQSAIRRIADKLRSLGYVEDDSIKQQPSAPEQTLVTSPGEIFVPLPNRIPKYRVGHTLDPSWSTPENPVPEPGSGNAIRRYHELRREVWKEKKEEKAKRSVEGNTESENVPTMAELKLPPAELKRLRGLGIAVKQKLKIGKAGITEGIVNGIHERWRNTELVKIVCEDMCRLNMRRTHDLLERKTGGLVVWRSGSIIILYRGSDYN...

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_024025`
TK1151 ID	TkA06G186120
OH-1004 ID	LXL04_024025
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.200
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

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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_024025

Location Chr05:78138554-78142665 (-)

Description Similar to CFM2: CRM-domain containing factor CFM2, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g01370`	Binds specific group II introns in chloroplasts and facilitates their splicing.	A CRM domain protein functions dually in group I and group II intron splicing in land plant chloroplasts.2007 · DOI: 10.1105/tpc.107.055160
`At3g23070`	Binds specific group II introns in chloroplasts and facilitates their splicing.	No verified direct reference in this release
`At4g14510`	Binds specific group II introns in chloroplasts and facilitates their splicing.	The bRPS6-Family Protein RFC3 Prevents Interference by the Splicing Factor CFM3b during Plastid rRNA Biogenesis in Arabidopsis thaliana .2020 · DOI: 10.3390/plants9030328

Rice

Reference gene ID	Possible function	Papers / DOI
`Os11g0592400`	Binds specific group II introns in chloroplasts and facilitates their splicing.	Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts.2008 · DOI: 10.1261/rna.1223708

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_024025 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000372 Group I intron splicing Biological Process

GO:0000373 Group II intron splicing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0048316 seed development Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009532 plastid stroma Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:1990904 ribonucleoprotein complex Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT3G01370

ath:AT3G23070

dosa:Os11g0592400

zma:100126360

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.

Plastid0.859

Rank 1 · LXL04_024025 · OH-1004

Nucleus0.102

Rank 2 · LXL04_024025 · OH-1004

Mitochondrion0.097

Rank 3 · LXL04_024025 · OH-1004

Cytoplasm0.057

Rank 4 · LXL04_024025 · OH-1004

Peroxisome0.018

Rank 5 · LXL04_024025 · 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.

PF01985.27CRS1_YhbY172-255 aa

PF01985.27CRS1_YhbY379-463 aa

PF01985.27CRS1_YhbY562-650 aa

PF01985.27CRS1_YhbY807-893 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024025	`PF01985.27`	CRS1_YhbY	172	255	1.5e-78	259.9
LXL04_024025	`PF01985.27`	CRS1_YhbY	379	463	1.5e-78	259.9
LXL04_024025	`PF01985.27`	CRS1_YhbY	562	650	1.5e-78	259.9
LXL04_024025	`PF01985.27`	CRS1_YhbY	807	893	1.5e-78	259.9

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
`Q8L7C2`	Arabidopsis thaliana	CRM-domain containing factor CFM2, chloroplastic	53.988%	Swiss-Prot	strong database homology
`F4J2U9`	Arabidopsis thaliana	CRM-domain containing factor CFM3A, chloroplastic/mitochondrial	40.323%	Swiss-Prot	moderate database homology
`F4JVH1`	Arabidopsis thaliana	CRM-domain containing factor CFM3B, chloroplastic	38.504%	Swiss-Prot	moderate database homology
`Q2R1U8`	Oryza sativa subsp. japonica	CRM-domain containing factor CFM3, chloroplastic/mitochondrial	46.218%	Swiss-Prot	moderate database homology

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