LXL04_012916 | RubberDandelionOmics

Gene overview

LXL04_012916

Reference: OH-1004 Chr: Chr03 Coordinates: 20802467-20804615 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1192 bp · LXL04_012916|LXL04_012916|OH1004|cDNA

TCGGCCCATTTCCATAGGGCCCGCTCGATAAAATGGCTCCAAAAACAAGTCCTGGCTTGCTCAGATCCTTTCCCGCCAGTTCTTCATTCACTGTCACCGGCACACATCCTCTTCCAGACCTTGAAAGATGCTGTGGGTGGACAAATACAGGCCAAAATCCCTCGACAAGGTTCTTGTACATGAAGATATCGCTCAAAATCTCAAGAAATTGGTCACGGAGCAGGATTGCCCACACTTACTGTTCTATGGCCCATCCGGTT...

CDS

Download CDS FASTA

1065 bp · LXL04_012916|LXL04_012916|OH1004|CDS

ATGCTGTGGGTGGACAAATACAGGCCAAAATCCCTCGACAAGGTTCTTGTACATGAAGATATCGCTCAAAATCTCAAGAAATTGGTCACGGAGCAGGATTGCCCACACTTACTGTTCTATGGCCCATCCGGTTCCGGGAAGAAAACCCTAATTATGGCCCTTCTCAGGCAGATGTTCGGGGCTGGTGCCGAGAAGGTGAAAGTGGAGAACAAAAACTGGAAAGTTGATGCTGGAAGCAGAACTATCGATTTGGAACTCAC...

Protein

Download Protein FASTA

354 aa · LXL04_012916|LXL04_012916|OH1004|PROTEIN

MLWVDKYRPKSLDKVLVHEDIAQNLKKLVTEQDCPHLLFYGPSGSGKKTLIMALLRQMFGAGAEKVKVENKNWKVDAGSRTIDLELTTLSSTNHVELNPSDAGFQDRYVVQEIIKEMAKNRPIDTKGKKTFKVLVLNEVDKLSREAQHSLRRTMEKYSASCRLILCCDSSSKVTEAVRSRCLNIRVNAPKEDQIVKVLEFIGKKEGLQLPPGFAARIAEKSGRSLRRAILSFETCRVKQYPFTNNQVIPPMDWEEYVCEI...

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_012916`
TK1151 ID	TkA02G530740
OH-1004 ID	LXL04_012916
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	100.000
Protein coverage (%)	TK1151 97.297 / OH-1004 71.186 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_012916

Location Chr03:20802467-20804615 (+)

Description Similar to RFC3: Replication factor C subunit 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g27740`	May be involved in DNA replication and thus regulate cell proliferation.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0792600`	May be involved in DNA replication and thus regulate cell proliferation.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012916 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006260 DNA replication Biological Process

GO:0006261 DNA-templated DNA replication Biological Process

GO:0006271 DNA strand elongation involved in DNA replication Biological Process

GO:0006272 leading strand elongation Biological Process

GO:0006281 DNA repair Biological Process

GO:1900264 positive regulation of DNA-directed DNA polymerase activity Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005663 DNA replication factor C complex Cellular Component

GO:0031389 Rad17 RFC-like complex Cellular Component

GO:0031390 Ctf18 RFC-like complex Cellular Component

GO:0031391 Elg1 RFC-like complex Cellular Component

KEGG gene cross-reference

ath:AT5G27740

bta:515602

ddi:DDB_G0293702

dosa:Os03g0792600

mmu:69263

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.

Nucleus0.918

Rank 1 · LXL04_012916 · OH-1004

Cytoplasm0.158

Rank 2 · LXL04_012916 · OH-1004

Cell membrane0.023

Rank 3 · LXL04_012916 · OH-1004

Mitochondrion0.019

Rank 4 · LXL04_012916 · OH-1004

Endoplasmic reticulum0.012

Rank 5 · LXL04_012916 · 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.

PF03215.22Rad172-58 aa

PF13177.13DNA_pol3_delta218-187 aa

PF00004.36AAA37-182 aa

PF21960.3RCF1-5-like_lid196-236 aa

PF22534.3RFC_C253-347 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012916	`PF03215.22`	Rad17	2	58	8e-06	26.6
LXL04_012916	`PF13177.13`	DNA_pol3_delta2	18	187	7.6e-11	43.0
LXL04_012916	`PF00004.36`	AAA	37	182	8.7e-07	30.2
LXL04_012916	`PF21960.3`	RCF1-5-like_lid	196	236	9.9e-10	38.9
LXL04_012916	`PF22534.3`	RFC_C	253	347	1.3e-34	119.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8VXX4`	Arabidopsis thaliana	Replication factor C subunit 3	88.136%	Swiss-Prot	strong database homology
`Q852K3`	Oryza sativa subsp. japonica	Replication factor C subunit 5	83.333%	Swiss-Prot	strong database homology

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