LXL04_012674 | RubberDandelionOmics

Gene overview

LXL04_012674

Reference: OH-1004 Chr: Chr03 Coordinates: 16682198-16684574 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

933 bp · LXL04_012674|LXL04_012674|OH1004|cDNA

ATGAATAATTCGATTAGACCGTGGAACCACTCTCCGTCTGTTCTTTCAAGCTCCGATTGGAACAGCCGCGCTCCTCTCAGCTTCTCGCCGTCTTCAACAACCACACCTCCTCGAAACGACAAGGTAACTTTCAAAACCTTAACAATTTGTATCCATTGTGTGATTAATCGACTGTTTGACCCTTTATGCCCAAAAACGGAATCCTTTTGTCACTTGAAATACTTCACCATGGCTATGCTGTTCAAGGatccaaacaagat...

CDS

Download CDS FASTA

933 bp · LXL04_012674|LXL04_012674|OH1004|CDS

ATGAATAATTCGATTAGACCGTGGAACCACTCTCCGTCTGTTCTTTCAAGCTCCGATTGGAACAGCCGCGCTCCTCTCAGCTTCTCGCCGTCTTCAACAACCACACCTCCTCGAAACGACAAGGTAACTTTCAAAACCTTAACAATTTGTATCCATTGTGTGATTAATCGACTGTTTGACCCTTTATGCCCAAAAACGGAATCCTTTTGTCACTTGAAATACTTCACCATGGCTATGCTGTTCAAGGATCCAAACAAGAT...

Protein

Download Protein FASTA

310 aa · LXL04_012674|LXL04_012674|OH1004|PROTEIN

MNNSIRPWNHSPSVLSSSDWNSRAPLSFSPSSTTTPPRNDKVTFKTLTICIHCVINRLFDPLCPKTESFCHLKYFTMAMLFKDPNKISAYRDRRFPGTQEEYEHALQTSTTVYIGNMSFYTTEEQLYELFSRAGEIKKIVMGLDKNTKTPCGFCFIMYYSREDTEDSVKYISGTILDDRPIRVDFDWGFQDGRQWGRGRSGGQLEEQRQVVDYGVGSLGSFQPPPMAANYGRHGGGGHGYGGSNRHGRGGDYQRKRYRDD...

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_012674`
TK1151 ID	TkA02G546120
OH-1004 ID	LXL04_012674
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	90.800
Protein coverage (%)	TK1151 88.475 / OH-1004 76.774 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_012674

Location Chr03:16682198-16684574 (+)

Description Similar to CBP20: Nuclear cap-binding protein subunit 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g44200`	Component of the cap-binding complex (CBC), which binds co- transcriptionally to the 5' cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing and RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs).	Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana.2008 · DOI: 10.1073/pnas.0802493105 Two cap-binding proteins CBP20 and CBP80 are involved in processing primary MicroRNAs.2008 · DOI: 10.1093/pcp/pcn146 FRIGIDA delays flowering in Arabidopsis via a cotranscriptional mechanism involving direct interaction with the nuclear cap-binding complex.2009 · DOI: 10.1104/pp.109.137448

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0612300`	Component of the cap-binding complex (CBC), which binds co-transcriptionally to the 5' cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing and RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs).	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_012674 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Biological Process

GO:0000380 alternative mRNA splicing, via spliceosome Biological Process

GO:0000394 RNA splicing, via endonucleolytic cleavage and ligation Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0000956 nuclear-transcribed mRNA catabolic process Biological Process

GO:0002191 cap-dependent translational initiation Biological Process

GO:0006406 mRNA export from nucleus Biological Process

GO:0006408 snRNA export from nucleus Biological Process

GO:0006446 regulation of translational initiation Biological Process

GO:0008334 histone mRNA metabolic process Biological Process

GO:0008380 RNA splicing Biological Process

GO:0016070 RNA metabolic process Biological Process

KEGG gene cross-reference

ath:AT5G44200

bta:510872

dosa:Os02g0612300

hsa:22916

isc:8026041

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.

Nucleus0.741

Rank 1 · LXL04_012674 · OH-1004

Cytoplasm0.385

Rank 2 · LXL04_012674 · OH-1004

Mitochondrion0.031

Rank 3 · LXL04_012674 · OH-1004

Cell membrane0.026

Rank 4 · LXL04_012674 · OH-1004

Endoplasmic reticulum0.023

Rank 5 · LXL04_012674 · 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.

PF00076.29RRM_1112-182 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012674	`PF00076.29`	RRM_1	112	182	6.1e-14	52.4

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
`Q9XFD1`	Arabidopsis thaliana	Nuclear cap-binding protein subunit 2	69.008%	Swiss-Prot	strong database homology
`Q84L14`	Oryza sativa subsp. japonica	Nuclear cap-binding protein subunit 2	63.415%	Swiss-Prot	strong database homology

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