TkA08G142230 | RubberDandelionOmics

Gene overview

TkA08G142230

Reference: TK1151 Chr: Chr08 Coordinates: 37081777-37088891 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2874 bp · TkA08G142230|TK1151|cDNA

GGCGATCAAAAGATCTCCATGGCTTAGTAAGCATTTTTCATGAAGTTACTCAGCAAACCGTATTGCAATGTTCAGTTTTGCGAATGATCAATTTTTGCTAGAATCGTTATCTTAATTCTTAACAATTTTAAGGAAATTTTACAATAAATCAAAGCTGTAGGTCGATTGAGGCCCCCAAATCAAAGAAGATCATGGGAGTTTTCCGTTTGCATACCCAGTGAGTTTACGGTTAAAGTGGATTCCTGTAATGGCGTCTAGAT...

CDS

Download CDS FASTA

1533 bp · TkA08G142230|TK1151|CDS

ATGGCGTCTAGATCGTCTGGTTTTTCAGGCATACAACTCGAGATCGAGTTGATGGACGCAGGGAAGAGGCTATTACTTCTGCCATCTTCATTTTCAGATGTTCTCGACGTTCTTGCACATATGGAGCGAACTCTATCCAAAGTGCAACAAGTGCCATCCGAATCAATGAAGTATGCCCTGCATCCAATAATCGATGCACTAATAGCCAAAGAACTGGTAATACATCCGGATACGAATGTAAACATCTTAGTTTCATGTTG...

Protein

Download Protein FASTA

510 aa · TkA08G142230|TK1151|PROTEIN

MASRSSGFSGIQLEIELMDAGKRLLLLPSSFSDVLDVLAHMERTLSKVQQVPSESMKYALHPIIDALIAKELVIHPDTNVNILVSCCISEILRIMAPNSPYNNQQMKDFFELATMTFEKLSSSSSGCYAKMTKVLQIFTTVRLPVIMLDLQLDKLVVRLFKQFLTVADFNYSEVIVEMEKIMTMIIEESEQPKIELVGLLVMSVRNYNQINSPVSWQLGEKVLKKCASKLKHQLPDFVQKMGIHLLDYSKVVSDICIGMP...

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	`TkA08G142230`
TK1151 ID	TkA08G142230
OH-1004 ID	LXL04_032021
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.500
Protein coverage (%)	TK1151 85.686 / OH-1004 46.243 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA08G142230

Location Chr08:37081777-37088891 (+)

Description Similar to SDF2: Stromal cell-derived factor 2-like protein

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g80810`	Cohesin cofactor dispensable during the meiotic division but playing an important role in DNA repair by homologous recombination (HR) probably by helping SMC5/SMC6 complex.	No verified direct reference in this release
`At1g15940`	Cohesin cofactor dispensable during the meiotic division but playing an important role in DNA repair by homologous recombination (HR) probably by helping SMC5/SMC6 complex.	Involvement of the Cohesin Cofactor PDS5 (SPO76) During Meiosis and DNA Repair in Arabidopsis thaliana.2015 · DOI: 10.3389/fpls.2015.01034
`At4g31880`	Cohesin cofactor dispensable during the meiotic division but playing an important role in DNA repair by homologous recombination (HR) probably by helping SMC5/SMC6 complex.	Involvement of the Cohesin Cofactor PDS5 (SPO76) During Meiosis and DNA Repair in Arabidopsis thaliana.2015 · DOI: 10.3389/fpls.2015.01034
`At5g47690`	Cohesin cofactor dispensable during the meiotic division but playing an important role in DNA repair by homologous recombination (HR) probably by helping SMC5/SMC6 complex.	Involvement of the Cohesin Cofactor PDS5 (SPO76) During Meiosis and DNA Repair in Arabidopsis thaliana.2015 · DOI: 10.3389/fpls.2015.01034
`At1g77600`	Cohesin cofactor dispensable during the meiotic division but playing an important role in DNA repair by homologous recombination (HR) probably by helping SMC5/SMC6 complex.	Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants.2014 · DOI: 10.1111/tpj.12595 Involvement of the Cohesin Cofactor PDS5 (SPO76) During Meiosis and DNA Repair in Arabidopsis thaliana.2015 · DOI: 10.3389/fpls.2015.01034

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032021 · 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:0002221 pattern recognition receptor signaling pathway Biological Process

GO:0006281 DNA repair Biological Process

GO:0006310 DNA recombination Biological Process

GO:0007064 mitotic sister chromatid cohesion Biological Process

GO:0009556 microsporogenesis Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0035825 homologous recombination Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0051301 cell division Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G80810

ath:AT2G25110

ath:AT4G31880

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.

Nucleus0.748

Rank 1 · TkA08G142230 · TK1151

Cytoplasm0.274

Rank 2 · TkA08G142230 · TK1151

Cell membrane0.061

Rank 3 · TkA08G142230 · TK1151

Endoplasmic reticulum0.039

Rank 4 · TkA08G142230 · TK1151

Golgi apparatus0.022

Rank 5 · TkA08G142230 · TK1151

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.

PF20168PDS534-260 aa

PF04716ETC_C1_NDUFA540-56 aa

PF00990GGDEF194-234 aa

PF04716ETC_C1_NDUFA5248-292 aa

PF21743PTM_DIR17_Tudor336-380 aa

PF09465LBR_tudor342-381 aa

PF05278PEARLI-4377-437 aa

PF20168PDS5406-424 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA08G142230	`PF20168`	PDS5	34	260	1.1e-38	133.5
TkA08G142230	`PF04716`	ETC_C1_NDUFA5	40	56	0.13	12.8
TkA08G142230	`PF00990`	GGDEF	194	234	0.2	12.2
TkA08G142230	`PF04716`	ETC_C1_NDUFA5	248	292	0.13	12.8
TkA08G142230	`PF21743`	PTM_DIR17_Tudor	336	380	6.1e-07	29.9
TkA08G142230	`PF09465`	LBR_tudor	342	381	0.00037	20.9
TkA08G142230	`PF05278`	PEARLI-4	377	437	3.7e-07	30.7
TkA08G142230	`PF20168`	PDS5	406	424	1.1e-38	133.5
TkA08G142230	`PF21743`	PTM_DIR17_Tudor	406	414	6.1e-07	29.9

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.

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Protein	Organism	Description	Identity	Database	Confidence
`A8MRD9`	Arabidopsis thaliana	sp\|A8MRD9\|PDS5D_ARATH Sister chromatid cohesion protein PDS5 homolog D	40.200%	Swiss-Prot	Low
`Q9S9P0`	Arabidopsis thaliana	sp\|Q9S9P0\|PDS5E_ARATH Sister chromatid cohesion protein PDS5 homolog E	36.900%	Swiss-Prot	Medium
`Q8GUP3`	Arabidopsis thaliana	sp\|Q8GUP3\|PDS5C_ARATH Sister chromatid cohesion protein PDS5 homolog C	57.400%	Swiss-Prot	Low
`B6EUB3`	Arabidopsis thaliana	sp\|B6EUB3\|PDS5A_ARATH Sister chromatid cohesion protein PDS5 homolog A	45.900%	Swiss-Prot	Low
`F4I735`	Arabidopsis thaliana	sp\|F4I735\|PDS5B_ARATH Sister chromatid cohesion protein PDS5 homolog B	28.800%	Swiss-Prot	Low

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