TkA07G298500 | RubberDandelionOmics

Gene overview

TkA07G298500

Reference: TK1151 Chr: Chr07 Coordinates: 74993396-74998205 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3107 bp · TkA07G298500|TK1151|cDNA

AAAGAAATAAATCATACGAATCTGGTTTAGAAAAAGGGAGCATTTACTTTTGAAAACTGCAGATGAGTATCTTATTTTTTAACTGTTTAAATACCTACAAAATTGCTCAAATCTGCATACTTGTTCCCCTTAGATTTCCTCAATTTTCTCAATCTCTTCCAACCCCGATTCAAATTTCACACAAGCAAGCCCTAATTCCCCCTTTTTTATATCTCTATCTCTGTATCTATTATTTATCTCTCTATATCGGACATAAACGA...

CDS

Download CDS FASTA

1017 bp · TkA07G298500|TK1151|CDS

ATGCTAGATGCACTCAAACCATCAATGAGGGCATTGATTCACGACAGTCTTTCATCACATTCAGATGTTGATGTTAAGGTTGCAGTCGCTTCATGCATCAGTGAAATAACAAGAATTACAGCACCAGATGCACCCTACAATGATGACCAAATGAGGGATGTATTTCAGTTGATTGTTTCTTCTTTTGAGGGTTTAGCTGACCAATCTAGCCGATCCTACAACAAAAGGGCATCAATTCTTGAGACTGTTTCAAAAGTTAG...

Protein

Download Protein FASTA

338 aa · TkA07G298500|TK1151|PROTEIN

MLDALKPSMRALIHDSLSSHSDVDVKVAVASCISEITRITAPDAPYNDDQMRDVFQLIVSSFEGLADQSSRSYNKRASILETVSKVRSCVIMLDLECEGLIVEMFEYFLRSVRDYHLESIYLSMENIMVLVLEESEEISVDLLKPILASVKKDSEGVLPIARKLAEGVLLKSASKVKPYLMPAVESIGDTLDMYTQAVASICEETTATIEHNDENASGVQLANESKSTKGSVDETQQGDESKLTTASSDHTDQVAKEETE...

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	`TkA07G298500`
TK1151 ID	TkA07G298500
OH-1004 ID	LXL04_029300
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	93.500
Protein coverage (%)	TK1151 88.757 / OH-1004 34.881 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA07G298500

Location Chr07:74993396-74998205 (-)

Description Similar to pds5b-b: Sister chromatid cohesion protein PDS5 homolog B-B

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`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
`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_029300 · 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: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:0009954 proximal/distal pattern formation Biological Process

GO:0009965 leaf morphogenesis Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0035825 homologous recombination Biological Process

GO:0051301 cell division Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

KEGG gene cross-reference

ath:AT1G15940

ath:AT1G77600

ath:AT4G31880

ath:AT5G47690

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.832

Rank 1 · TkA07G298500 · TK1151

Cytoplasm0.230

Rank 2 · TkA07G298500 · TK1151

Cell membrane0.053

Rank 3 · TkA07G298500 · TK1151

Endoplasmic reticulum0.036

Rank 4 · TkA07G298500 · TK1151

Golgi apparatus0.020

Rank 5 · TkA07G298500 · 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.

PF20168PDS53-180 aa

PF02862DDHD159-304 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G298500	`PF20168`	PDS5	3	180	1.5e-48	166.2
TkA07G298500	`PF02862`	DDHD	159	304	4.9	8.0

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
`Q8GUP3`	Arabidopsis thaliana	sp\|Q8GUP3\|PDS5C_ARATH Sister chromatid cohesion protein PDS5 homolog C	52.400%	Swiss-Prot	High
`Q9S9P0`	Arabidopsis thaliana	sp\|Q9S9P0\|PDS5E_ARATH Sister chromatid cohesion protein PDS5 homolog E	52.600%	Swiss-Prot	Medium
`A8MRD9`	Arabidopsis thaliana	sp\|A8MRD9\|PDS5D_ARATH Sister chromatid cohesion protein PDS5 homolog D	49.300%	Swiss-Prot	Medium
`B6EUB3`	Arabidopsis thaliana	sp\|B6EUB3\|PDS5A_ARATH Sister chromatid cohesion protein PDS5 homolog A	49.700%	Swiss-Prot	Medium
`F4I735`	Arabidopsis thaliana	sp\|F4I735\|PDS5B_ARATH Sister chromatid cohesion protein PDS5 homolog B	31.600%	Swiss-Prot	Medium

JBrowse

View in Genome Browser

Gene Card