LXL04_022923 | RubberDandelionOmics

Gene overview

LXL04_022923

Reference: OH-1004 Chr: Chr05 Coordinates: 13705129-13709681 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2538 bp · LXL04_022923|LXL04_022923|OH1004|cDNA

ATGGCTCTGGTACCCACTCGCCTAGACTCGTTTCACAGCTCAGTGTACAAGCTCCATTTCTTCAGGTACTGCTCCTATAACCCTTTCAAGAAACACAAAGTCATTGCAAATTATGAGAGTAATTCGACAAATTTAAACCCAACACCCcataaaaaatccaaaattgTTCTTAGAAACAAGAACAACGAAGCCAGTTCTATCGCAGAATCACCGATTTTACAGTCAAAAAGTAACCCTAGCGGTGGGTGGTTAGAGAAATG...

CDS

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2538 bp · LXL04_022923|LXL04_022923|OH1004|CDS

ATGGCTCTGGTACCCACTCGCCTAGACTCGTTTCACAGCTCAGTGTACAAGCTCCATTTCTTCAGGTACTGCTCCTATAACCCTTTCAAGAAACACAAAGTCATTGCAAATTATGAGAGTAATTCGACAAATTTAAACCCAACACCCCATAAAAAATCCAAAATTGTTCTTAGAAACAAGAACAACGAAGCCAGTTCTATCGCAGAATCACCGATTTTACAGTCAAAAAGTAACCCTAGCGGTGGGTGGTTAGAGAAATG...

Protein

Download Protein FASTA

845 aa · LXL04_022923|LXL04_022923|OH1004|PROTEIN

MALVPTRLDSFHSSVYKLHFFRYCSYNPFKKHKVIANYESNSTNLNPTPHKKSKIVLRNKNNEASSIAESPILQSKSNPSGGWLEKWDDTHNQNWPKKAEPVLNYRYRDDTENSDYENNYDSDADGAHGTGSGSTMDRIVEKLKKFGYVDDVKEKKEREIEKGSIEDIFYVEEGILPNSRGGFSPESPLGIEDVFRGSNGKVRFPWEKPSPEDDANRNSVRQKSKTCVAELTIPESELRRLRNLAFRLKNKTRITGAGVT...

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_022923`
TK1151 ID	TkA06G427600
OH-1004 ID	LXL04_022923
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.500
Protein coverage (%)	TK1151 96.916 / OH-1004 26.036 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_022923

Location Chr05:13705129-13709681 (+)

Description Similar to CFM3A: CRM-domain containing factor CFM3A, chloroplastic/mitochondrial

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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

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_022923 · 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:0006364 rRNA processing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0042794 plastid rRNA transcription 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:0009536 plastid Cellular Component

GO:0009570 chloroplast stroma Cellular Component

KEGG gene cross-reference

ath:AT3G01370

ath:AT3G23070

ath:AT4G14510

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.

Plastid0.826

Rank 1 · LXL04_022923 · OH-1004

Mitochondrion0.131

Rank 2 · LXL04_022923 · OH-1004

Nucleus0.086

Rank 3 · LXL04_022923 · OH-1004

Cytoplasm0.044

Rank 4 · LXL04_022923 · OH-1004

Peroxisome0.016

Rank 5 · LXL04_022923 · 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.

PF01985.27CRS1_YhbY235-316 aa

PF01985.27CRS1_YhbY421-503 aa

PF01985.27CRS1_YhbY635-722 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022923	`PF01985.27`	CRS1_YhbY	235	316	1.9e-56	189.0
LXL04_022923	`PF01985.27`	CRS1_YhbY	421	503	1.9e-56	189.0
LXL04_022923	`PF01985.27`	CRS1_YhbY	635	722	1.9e-56	189.0

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
`F4J2U9`	Arabidopsis thaliana	CRM-domain containing factor CFM3A, chloroplastic/mitochondrial	58.699%	Swiss-Prot	strong database homology
`F4JVH1`	Arabidopsis thaliana	CRM-domain containing factor CFM3B, chloroplastic	55.838%	Swiss-Prot	strong database homology
`Q8L7C2`	Arabidopsis thaliana	CRM-domain containing factor CFM2, chloroplastic	39.752%	Swiss-Prot	moderate database homology
`Q2R1U8`	Oryza sativa subsp. japonica	CRM-domain containing factor CFM3, chloroplastic/mitochondrial	54.570%	Swiss-Prot	strong database homology

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