LXL04_026477 | RubberDandelionOmics

Gene overview

LXL04_026477

Reference: OH-1004 Chr: Chr05 Coordinates: 126935170-126937179 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1002 bp · LXL04_026477|LXL04_026477|OH1004|cDNA

ATggcttcttcatcatcttcaatgTTAAGCCATGGCTACGAAATTCCATGGGTTGAGAAGTTCAGACCTACAAAGGTGGCAGACATTGTCGGGAACGAAGAAGCCGTCTCCAGGCTTCAAGTAATTGCGCACGATGGTAACATGCCCAATCTCATATTAGCTGGTCCTCCTGGAACAGGTAAGACCACAAGCATATTAGCTCTTGCACATGAGTTACTTGGACCAAATTACAAAGAGGCAGTTTTAGAGCTCAATGCATC...

CDS

Download CDS FASTA

1002 bp · LXL04_026477|LXL04_026477|OH1004|CDS

ATGGCTTCTTCATCATCTTCAATGTTAAGCCATGGCTACGAAATTCCATGGGTTGAGAAGTTCAGACCTACAAAGGTGGCAGACATTGTCGGGAACGAAGAAGCCGTCTCCAGGCTTCAAGTAATTGCGCACGATGGTAACATGCCCAATCTCATATTAGCTGGTCCTCCTGGAACAGGTAAGACCACAAGCATATTAGCTCTTGCACATGAGTTACTTGGACCAAATTACAAAGAGGCAGTTTTAGAGCTCAATGCATC...

Protein

Download Protein FASTA

333 aa · LXL04_026477|LXL04_026477|OH1004|PROTEIN

MASSSSSMLSHGYEIPWVEKFRPTKVADIVGNEEAVSRLQVIAHDGNMPNLILAGPPGTGKTTSILALAHELLGPNYKEAVLELNASDDRGIDVVRNKIKMFAQKKVTLPPGRHKVIILDEADSMTSGAQQALRRTMEIYSNSTRFALACNTSAKIIEPIQSRCALVRFSRLSDQEILGRLMCVVDAEKVAYVPEGLEAIIFTADGDMRQALNNLQATFTGFRFVNQENVFKVCDQPHPLHVKNMVRNVLEGKFDDACSG...

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_026477`
TK1151 ID	TkA06G011820
OH-1004 ID	LXL04_026477
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_026477

Location Chr05:126935170-126937179 (+)

Description Similar to RFC2: Replication factor C subunit 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g63160`	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
`Os04g0569000`	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_026477 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000076 DNA replication checkpoint signaling Biological Process

GO:0006260 DNA replication Biological Process

GO:0006261 DNA-templated DNA replication 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:0003677 DNA binding Molecular Function

GO:0003689 DNA clamp loader activity Molecular Function

KEGG gene cross-reference

ath:AT1G63160

bta:508652

dosa:Os04g0569000

hsa:5982

rno:116468

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.

Nucleus0.775

Rank 1 · LXL04_026477 · OH-1004

Cytoplasm0.278

Rank 2 · LXL04_026477 · OH-1004

Mitochondrion0.044

Rank 3 · LXL04_026477 · OH-1004

Cell membrane0.032

Rank 4 · LXL04_026477 · OH-1004

Endoplasmic reticulum0.020

Rank 5 · LXL04_026477 · 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.

PF01078.28Mg_chelatase27-86 aa

PF25199.2nSTAND_NTPase534-153 aa

PF13173.13AAA_1450-149 aa

PF00004.36AAA51-168 aa

PF13177.13DNA_pol3_delta292-172 aa

PF08542.17Rep_fac_C237-322 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026477	`PF01078.28`	Mg_chelatase	27	86	4.2e-06	27.0
LXL04_026477	`PF25199.2`	nSTAND_NTPase5	34	153	1.5e-06	28.8
LXL04_026477	`PF13173.13`	AAA_14	50	149	9.4e-07	29.6
LXL04_026477	`PF00004.36`	AAA	51	168	3.6e-14	54.0
LXL04_026477	`PF13177.13`	DNA_pol3_delta2	92	172	6e-10	40.1
LXL04_026477	`PF08542.17`	Rep_fac_C	237	322	3.1e-24	85.9

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
`Q9CAM7`	Arabidopsis thaliana	Replication factor C subunit 2	90.361%	Swiss-Prot	strong database homology
`Q7XRX1`	Oryza sativa subsp. japonica	Replication factor C subunit 4	84.639%	Swiss-Prot	strong database homology

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