LXL04_013704 | RubberDandelionOmics

Gene overview

LXL04_013704

Reference: OH-1004 Chr: Chr03 Coordinates: 34469863-34472808 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2271 bp · LXL04_013704|LXL04_013704|OH1004|cDNA

ATGGAGCTTTCTTGCATTTGGATAAATTTATCTCGCCACACCGCATTTCGACTTCCAAATTCAGCTTCGAGGCAAACCTGTTCGTGTTTGAGAATGTCAGCAATGATGTTTCTCTCACCCACCATGCTCTCAGATTCTTCGAACTTCCCCAAAAAGATTTACTCGTTAAACCCTCAAAATCATCCTAATTCCCTTTCTGTTCCTACCCAAACCACCCCTGAAATTCGTGACACAAATAATGAATTTAAGCTAAATCCTTC...

CDS

Download CDS FASTA

2271 bp · LXL04_013704|LXL04_013704|OH1004|CDS

ATGGAGCTTTCTTGCATTTGGATAAATTTATCTCGCCACACCGCATTTCGACTTCCAAATTCAGCTTCGAGGCAAACCTGTTCGTGTTTGAGAATGTCAGCAATGATGTTTCTCTCACCCACCATGCTCTCAGATTCTTCGAACTTCCCCAAAAAGATTTACTCGTTAAACCCTCAAAATCATCCTAATTCCCTTTCTGTTCCTACCCAAACCACCCCTGAAATTCGTGACACAAATAATGAATTTAAGCTAAATCCTTC...

Protein

Download Protein FASTA

756 aa · LXL04_013704|LXL04_013704|OH1004|PROTEIN

MELSCIWINLSRHTAFRLPNSASRQTCSCLRMSAMMFLSPTMLSDSSNFPKKIYSLNPQNHPNSLSVPTQTTPEIRDTNNEFKLNPSIPATKTAPWMKGPLILEPNQVIDFSKPKTRKKSSDNKNEKAEKSLTHKVSGGRGKHAMKKILYSIDTLEEETQELEDTQQNLAPIEFDLSLGKLGEDSDGGDKRWPRRKMPWEREERMVFRRTKREKTVTAADITLNEELLERLRAEARRMRKWVKVKKAGVNEGVLEQIRLI...

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_013704`
TK1151 ID	TkA02G477120
OH-1004 ID	LXL04_013704
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.700
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_013704

Location Chr03:34469863-34472808 (-)

Description Similar to At5g16180: Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g16180`	Required for the splicing of group IIA introns in chloroplasts, by regulating the intron folding.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0360100`	Required for the splicing of group IIA introns in chloroplasts, by regulating the intron folding.	No verified direct reference in this release
`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_013704 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000373 Group II intron splicing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006417 regulation of translation Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast 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:AT5G16180

dosa:Os08g0360100

dosa:Os11g0592400

zma:100126360

zma:541870

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.

Plastid0.809

Rank 1 · LXL04_013704 · OH-1004

Mitochondrion0.146

Rank 2 · LXL04_013704 · OH-1004

Nucleus0.087

Rank 3 · LXL04_013704 · OH-1004

Cytoplasm0.046

Rank 4 · LXL04_013704 · OH-1004

Peroxisome0.013

Rank 5 · LXL04_013704 · 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_YhbY223-306 aa

PF01985.27CRS1_YhbY400-484 aa

PF01985.27CRS1_YhbY613-700 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013704	`PF01985.27`	CRS1_YhbY	223	306	4e-51	172.0
LXL04_013704	`PF01985.27`	CRS1_YhbY	400	484	4e-51	172.0
LXL04_013704	`PF01985.27`	CRS1_YhbY	613	700	4e-51	172.0

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
`Q9LF10`	Arabidopsis thaliana	Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic	52.765%	Swiss-Prot	strong database homology
`Q6YYA3`	Oryza sativa subsp. japonica	Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic	41.102%	Swiss-Prot	moderate database homology
`Q2R1U8`	Oryza sativa subsp. japonica	CRM-domain containing factor CFM3, chloroplastic/mitochondrial	39.858%	Swiss-Prot	moderate database homology

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