TkA01G028970 | RubberDandelionOmics

Gene overview

TkA01G028970

Reference: TK1151 Chr: Chr01 Coordinates: 7442565-7450664 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

695 bp · TkA01G028970|TK1151|cDNA

CCCGCAGGTAAATCCATAGACTTATTATTAATCATGCATTCTAATTACCCTCATTGAAAGCATTTTCAGATTTCAAAATTTAAACTAAATTGATCAGCATGCTAAGATTTAACTGATTGTATGCAGGCTGGATACTTTTGCTCTGTTTGTGAATGTGTAGTTAAAGATTCTGCAAACTATCTGGACCATATCAATGGAAAGAAGCATCAAAGAGCATTAGGAATGTCTATGAGGGTAGAAAGGGCATCTCTTGAACAGGT...

CDS

Download CDS FASTA

1482 bp · TkA01G028970|TK1151|CDS

ATGGGTGTGGGTTTCAGGCTCAGTTTGAAATGGGGACTCTCACTTCAACCTCGTCTCTCTTCCAACCATTCATCTTTGCCGTTTTCCACATACGCATCCTTTAAAGGTAAAGATATCAATTATGATTTGGCGAGTGTATCTCTATCAATGGAAAGTGAGATTTCTTACAGTGATCCCATTAACGGAAGTACATGTTCTTCCGCTTCTCGAATCTTGGACATTGATTACTCGGAATCCCGTAAAATAAAGATTACTCTTAC...

Protein

Download Protein FASTA

493 aa · TkA01G028970|TK1151|PROTEIN

MGVGFRLSLKWGLSLQPRLSSNHSSLPFSTYASFKGKDINYDLASVSLSMESEISYSDPINGSTCSSASRILDIDYSESRKIKITLTKSCSFGRYVADSDVVTLEQDILDHLQKLGALKILHTSFSQIPKCPFSTNSIVTKKTAKPVVPSSRKVKRKSQRERTSRKADDDAGLVAFQIHSQPIIDRNNSRRVNFSSKRLSKSRSGKVKITRNEAELSRGVKNDVKKEVGPMVSFSSWAEAAGVDKKELLENLQFGWSCRD...

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	`TkA01G028970`
TK1151 ID	TkA01G028970
OH-1004 ID	LXL04_005624
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	89.700
Protein coverage (%)	TK1151 99.594 / OH-1004 98.687 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 TkA01G028970

Location Chr01:7442565-7450664 (-)

Description Similar to SIGC: RNA polymerase sigma factor sigC

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g53920`	Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released.	Characterization of Arabidopsis plastid sigma-like transcription factors SIG1, SIG2 and SIG3.2003 · DOI: 10.1023/a:1022095017355
`At1g08540`	Required for the transition of plastids into chloroplasts by coordinating nuclear and chloroplastic genomes under light conditions.	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_005624 · 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:0006352 DNA-templated transcription initiation Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006399 tRNA metabolic process Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0010114 response to red light Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0071482 cellular response to light stimulus Biological Process

GO:0071483 cellular response to blue light Biological Process

GO:0090351 seedling development Biological Process

GO:2001141 regulation of RNA biosynthetic process Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

KEGG gene cross-reference

ana:all5263

ath:AT1G08540

ath:AT2G36990

ath:AT3G53920

syf:Synpcc7942_0649

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.

Plastid0.703

Rank 1 · TkA01G028970 · TK1151

Mitochondrion0.155

Rank 2 · TkA01G028970 · TK1151

Nucleus0.111

Rank 3 · TkA01G028970 · TK1151

Cytoplasm0.026

Rank 4 · TkA01G028970 · TK1151

Cell membrane0.010

Rank 5 · TkA01G028970 · 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.

PF13384HTH_2362-76 aa

PF04542Sigma70_r2263-331 aa

PF04539Sigma70_r3342-416 aa

PF04545Sigma70_r4364-375 aa

PF04545Sigma70_r4431-482 aa

PF13384HTH_23446-476 aa

PF13560HTH_31450-475 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G028970	`PF13384`	HTH_23	62	76	0.25	12.0
TkA01G028970	`PF04542`	Sigma70_r2	263	331	3.2e-15	56.3
TkA01G028970	`PF04539`	Sigma70_r3	342	416	4.3e-06	27.4
TkA01G028970	`PF04545`	Sigma70_r4	364	375	7.9e-16	58.0
TkA01G028970	`PF04545`	Sigma70_r4	431	482	7.9e-16	58.0
TkA01G028970	`PF13384`	HTH_23	446	476	0.25	12.0
TkA01G028970	`PF13560`	HTH_31	450	475	0.052	14.6

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
`O24621`	Arabidopsis thaliana	sp\|O24621\|SIGC_ARATH RNA polymerase sigma factor sigC	46.000%	Swiss-Prot	Medium
`O22056`	Arabidopsis thaliana	sp\|O22056\|SIGB_ARATH RNA polymerase sigma factor sigB	38.200%	Swiss-Prot	Medium

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