TkA03G559510 | RubberDandelionOmics

Gene overview

TkA03G559510

Reference: TK1151 Chr: Chr03 Coordinates: 141844422-141849357 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3470 bp · TkA03G559510|TK1151|cDNA

GATTTCAATTCCGTACATCGGCCTCACTCTCGCGACGCGATGCATCCCAAATCCCCGATCGCGTGAGCCATTCGTCCACCCATCGCCGGCGCCGGAGACAGCAGCTACCAGGTAGCAGGTAGCACCCTCCCTCTTCGTCACTCTCTCAGTCTCGTTGTCTATCAGTCTCTCGATGTGACTCTCTGTAGCAGGGTTTTAGAAGGGTGTTAATACGTGCCATACTTACATACACGGAATCGGCGAGAAGAGAGTGCGTCTAA...

CDS

Download CDS FASTA

507 bp · TkA03G559510|TK1151|CDS

ATGGATGAGGTGGACGGGATGTCAGCTGGAGATAGAGGCGGTGTAGCCGACCTAATCGCCAGCATTAAAATCTCCAAAATCCCCATAATCTGCATATGCAATGATCGGTACAGTCAAAAGCTGAAAAGTCTAGTCAACTATTGTCTTCTGTTGACCTTCCGGAAGCCCACAAAACAACAGATGGCGAAAAGGCTAATGCAAGTTGCAAATGCGGAAAAGATTCAAGTGAATGAGGTGGCACTTGAAGAACTTTCGGAAAG...

Protein

Download Protein FASTA

168 aa · TkA03G559510|TK1151|PROTEIN

MDEVDGMSAGDRGGVADLIASIKISKIPIICICNDRYSQKLKSLVNYCLLLTFRKPTKQQMAKRLMQVANAEKIQVNEVALEELSERVNGDMRMALNQLQYMSLSMSVIKFDDVRQRLLTSSKDEDISPFTAVDKLFGYNAGKLRMDERFDLSMSDMDLVPLIIQEII

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	`TkA03G559510`
TK1151 ID	TkA03G559510
OH-1004 ID	LXL04_033298
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	30.000
Protein coverage (%)	TK1151 65.476 / OH-1004 11.620 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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA03G559510

Location Chr03:141844422-141849357 (-)

Description Similar to chtf18: Chromosome transmission fidelity protein 18 homolog

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g22010`	Plays a role as mediator of transcriptional gene silencing (TGS), DNA replication, DNA repair, hypersensitive response (HR) and telomere length regulation.	Arabidopsis replication factor C subunit 1 plays an important role in embryogenesis.2007 · PMID: 17556804 DNA replication factor C1 mediates genomic stability and transcriptional gene silencing in Arabidopsis.2010 · DOI: 10.1105/tpc.110.076349 Replication factor C1 (RFC1) is required for double-strand break repair during meiotic homologous recombination in Arabidopsis.2013 · DOI: 10.1111/tpj.12024 The DNA replication factor RFC1 is required for interference-sensitive meiotic crossovers in Arabidopsis thaliana.2012 · DOI: 10.1371/journal.pgen.1003039

Rice

Reference gene ID	Possible function	Papers / DOI
`Os11g0572100`	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_033298 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)

GO:0006260 DNA replication Biological Process

GO:0007062 sister chromatid cohesion Biological Process

GO:0007131 reciprocal meiotic recombination Biological Process

GO:0007140 male meiotic nuclear division Biological Process

GO:0045005 DNA-templated DNA replication maintenance of fidelity Biological Process

GO:0048468 cell development Biological Process

GO:0051985 negative regulation of chromosome segregation Biological Process

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

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005663 DNA replication factor C complex Cellular Component

KEGG gene cross-reference

dme:Dmel_CG33122

hsa:63922

mmu:214901

spo:2541270

xla:414577

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.

Nucleus0.892

Rank 1 · TkA03G559510 · TK1151

Cytoplasm0.167

Rank 2 · TkA03G559510 · TK1151

Mitochondrion0.031

Rank 3 · TkA03G559510 · TK1151

Cell membrane0.020

Rank 4 · TkA03G559510 · TK1151

Golgi apparatus0.010

Rank 5 · TkA03G559510 · TK1151

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.

PF21328Gp44_lid58-103 aa

PF25361AAA_lid_RFC159-115 aa

PF22608DNAX_ATPase_lid61-96 aa

PF27254HP_1247_M61-100 aa

PF21960RCF1-5-like_lid63-104 aa

PF16193AAA_assoc_272-106 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G559510	`PF21328`	Gp44_lid	58	103	0.0055	17.6
TkA03G559510	`PF25361`	AAA_lid_RFC1	59	115	2.1e-10	40.6
TkA03G559510	`PF22608`	DNAX_ATPase_lid	61	96	0.0047	17.4
TkA03G559510	`PF27254`	HP_1247_M	61	100	0.0077	16.9
TkA03G559510	`PF21960`	RCF1-5-like_lid	63	104	3.3e-08	34.1
TkA03G559510	`PF16193`	AAA_assoc_2	72	106	0.00037	21.4

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
`Q9C587`	Arabidopsis thaliana	sp\|Q9C587\|RFC1_ARATH Replication factor C subunit 1	86.100%	Swiss-Prot	High
`Q2R2B4`	Oryza sativa subsp. japonica	sp\|Q2R2B4\|RFC1_ORYSJ Replication factor C subunit 1	82.500%	Swiss-Prot	High

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