TkA02G540970 | RubberDandelionOmics

Gene overview

TkA02G540970

Reference: TK1151 Chr: Chr02 Coordinates: 139571523-139577159 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4449 bp · TkA02G540970|TK1151|cDNA

CTTGATGCACCGCGGGCTTATCACCAGTACTTACCATATACAATGATCCCAAGACTTTCCGACACACACTCTTTGACCTCTCTCTCTTTCTCTCTCCCCAAAAAAATTCATTCAAATCTCTTTCAAAGCAAATGCGCTTCACGCTTTCCCCATCTAAAACTCCAAAATAACCTCAACAATATTGAAAACACTTTGATTTCATTTCAAACTGCACCACTACTTATTCATAGCTGGTTGTTCGAGCTCGATGTCGTGATTCC...

CDS

Download CDS FASTA

3642 bp · TkA02G540970|TK1151|CDS

ATGTTTTATTCGCAGTTCATATTAGCAAAAAAGGGTCCTCTAGGGACAATATGGATAGCAGCACATCTAGAGAGGAAGCTCCGCAAGAATCAAGTTGCAGATACTGATATCGGCTTCTCTGTAGACTCGATTCTCTTCCCTGAAATGCCAATTGCACTCCGGTTATCCAGCCATCTTTTACTTGGTGTCGTTAGGATATACTCAAGAAAGGTAAATTACCTATTCGATGATTGCAGTGAAGCTTTACTTAAAGTAAAACA...

Protein

Download Protein FASTA

1213 aa · TkA02G540970|TK1151|PROTEIN

MFYSQFILAKKGPLGTIWIAAHLERKLRKNQVADTDIGFSVDSILFPEMPIALRLSSHLLLGVVRIYSRKVNYLFDDCSEALLKVKQAFRSTAVDLPPEESTAPYHSITLPETFDLDDFELPGSEIYQGNYVDHHVSSKEQITLQDTMEGVVYSTSNFGLDERFGDGDACGLDLDEQELMVEKAEHAIETSNSEAMPVPAGNIVNNQQIEEYDGENEPIEYAHAPCTPGLWEEPNLSNIQETSAYDDHQEPENHTITESA...

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	`TkA02G540970`
TK1151 ID	TkA02G540970
OH-1004 ID	LXL04_012734
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.300
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	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 TkA02G540970

Location Chr02:139571523-139577159 (+)

Description Similar to SYN4: Sister chromatid cohesion 1 protein 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g16270`	Involved in sister chromatid and centromere cohesion during mitosis.	Cohesin gene defects may impair sister chromatid alignment and genome stability in Arabidopsis thaliana.2009 · DOI: 10.1007/s00412-009-0220-x
`At3g59550`	May be involved in sister chromatid cohesion during mitosis.	No verified direct reference in this release
`At5g40840`	May be involved in sister chromatid cohesion during mitosis.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012734 · 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:0000278 mitotic cell cycle Biological Process

GO:0006302 double-strand break repair Biological Process

GO:0007059 chromosome segregation Biological Process

GO:0007062 sister chromatid cohesion Biological Process

GO:0009555 pollen development Biological Process

GO:0009561 megagametogenesis Biological Process

GO:0051301 cell division Biological Process

GO:0070601 centromeric sister chromatid cohesion Biological Process

GO:1990414 replication-born double-strand break repair via sister chromatid exchange Biological Process

GO:0000775 chromosome, centromeric region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

KEGG gene cross-reference

ath:AT3G59550

ath:AT5G16270

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.

Nucleus0.947

Rank 1 · TkA02G540970 · TK1151

Cytoplasm0.189

Rank 2 · TkA02G540970 · TK1151

Cell membrane0.016

Rank 3 · TkA02G540970 · TK1151

Mitochondrion0.016

Rank 4 · TkA02G540970 · TK1151

Endoplasmic reticulum0.008

Rank 5 · TkA02G540970 · 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.

PF04825Rad21_Rec8_N1-101 aa

PF04824Rad21_Rec81-12 aa

PF06278CNDH2_N59-87 aa

PF03925SeqA316-361 aa

PF06278CNDH2_N325-363 aa

PF03925SeqA573-594 aa

PF06278CNDH2_N1008-1045 aa

PF06278CNDH2_N1081-1101 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA02G540970	`PF04825`	Rad21_Rec8_N	1	101	1.8e-38	131.7
TkA02G540970	`PF04824`	Rad21_Rec8	1	12	1.1e-19	70.2
TkA02G540970	`PF06278`	CNDH2_N	59	87	0.41	11.4
TkA02G540970	`PF03925`	SeqA	316	361	0.2	12.5
TkA02G540970	`PF06278`	CNDH2_N	325	363	0.41	11.4
TkA02G540970	`PF03925`	SeqA	573	594	0.2	12.5
TkA02G540970	`PF06278`	CNDH2_N	1008	1045	0.41	11.4
TkA02G540970	`PF06278`	CNDH2_N	1081	1101	0.41	11.4
TkA02G540970	`PF04824`	Rad21_Rec8	1158	1204	1.1e-19	70.2

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
`Q8W1Y0`	Arabidopsis thaliana	sp\|Q8W1Y0\|SSC14_ARATH Sister chromatid cohesion 1 protein 4	37.600%	Swiss-Prot	Medium
`Q9FQ19`	Arabidopsis thaliana	sp\|Q9FQ19\|SCC13_ARATH Sister chromatid cohesion 1 protein 3	49.300%	Swiss-Prot	Low
`Q9FQ20`	Arabidopsis thaliana	sp\|Q9FQ20\|SCC12_ARATH Sister chromatid cohesion 1 protein 2	43.400%	Swiss-Prot	Low

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