TkA07G077740 | RubberDandelionOmics

Gene overview

TkA07G077740

Reference: TK1151 Chr: Chr07 Coordinates: 20235465-20245484 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4643 bp · TkA07G077740|TK1151|cDNA

GGAAACTCCAGTACTGTGATAAAAAAATTCAAAATGAGAAAACCCACACAAAACGTTAAAAAATCACTTGCTGCATGCTCCTTCTAGGCTAACACAAGAGAGGGGAGCCTTCACAAATCAGACCACTCTCTCTCTCCATAGACGCCTGTAAAACCCTCTCTTTCTCATCAATTTCACCATCGATCGATAAAGGTGTCTTTTCATGGTTTCTGAGCTAAACCTTACGCACATTTCGCAGTAGCATTTCAGTAAAATTAGGG...

CDS

Download CDS FASTA

5808 bp · TkA07G077740|TK1151|CDS

ATGATGGAAGAAAATCCAAATCCTGCTGTTTTAGAAGGGAAGATTACGGGGATTAGCTTTTCATTGGCCACACAACAAGAAATTTGCTTGGCTTCAATTAGTGATTGCCCCATTAGCCATGCAAGCCAGCTTTCAAACCCCTTTCTTGGACTTCCTCTAGAAGTTGGGAAGTGTGAATCTTGTGGTACAGCTGAACCAGGCAAATGTGAAGGTCATTTCGGGTATATAGAGTTGCCAATTCCAATATATCATCCGTCTCA...

Protein

Download Protein FASTA

1935 aa · TkA07G077740|TK1151|PROTEIN

MMEENPNPAVLEGKITGISFSLATQQEICLASISDCPISHASQLSNPFLGLPLEVGKCESCGTAEPGKCEGHFGYIELPIPIYHPSHLTELKRILSLICLKCLKFKNRRLQNKNSGMLERVLTVCCDEAACVTISEEKKEDGASYLQLKVPSKTCKDGLWDFLDRYGYRYGHGHKRPLLPSEVLVMLKKISESTKKKLAGRGCYFQEGYIMQHLPIPPNCLSTPDVSDGMNVMSSDISMTMLKKVLRQVEIIKSSRSGSP...

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	`TkA07G077740`
TK1151 ID	TkA07G077740
OH-1004 ID	LXL04_027604
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.200
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 TkA07G077740

Location Chr07:20235465-20245484 (+)

Description Similar to NRPE1: DNA-directed RNA polymerase V subunit 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g40030`	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	Atypical RNA polymerase subunits required for RNA-directed DNA methylation.2005 · DOI: 10.1038/ng1580 Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis.2005 · DOI: 10.1101/gad.348405 The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center.2006 · DOI: 10.1016/j.cell.2006.05.031 PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis.2008 · DOI: 10.1073/pnas.0709632105 NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis.2008 · DOI: 10.1111/j.1365-313x.2008.03525.x
`At1g63020`	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).	Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis.2005 · DOI: 10.1101/gad.348405 DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal.2005 · DOI: 10.1038/ng1675 Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis.2005 · DOI: 10.1016/j.cell.2005.11.035 An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis.2007 · DOI: 10.1105/tpc.107.051540 Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways.2007 · DOI: 10.1038/ng2081 Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis.2007 · DOI: 10.1073/pnas.0706701104 PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis.2008 · DOI: 10.1073/pnas.0709632105 NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis.2008 · DOI: 10.1111/j.1365-313x.2008.03525.x
`At4g35800`	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	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_027604 · 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:0006351 DNA-templated transcription Biological Process

GO:0006353 DNA-templated transcription termination Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006366 transcription by RNA polymerase II Biological Process

GO:0006367 transcription initiation at RNA polymerase II promoter Biological Process

GO:0006368 transcription elongation by RNA polymerase II Biological Process

GO:0006369 termination of RNA polymerase II transcription Biological Process

GO:0006370 7-methylguanosine mRNA capping Biological Process

GO:0019985 translesion synthesis Biological Process

GO:0030422 siRNA processing Biological Process

GO:0030643 intracellular phosphate ion homeostasis Biological Process

GO:0033120 positive regulation of RNA splicing Biological Process

KEGG gene cross-reference

ago:AGOS_ADR086C

ath:AT2G40030

bta:282312

hsa:5430

spo:2540292

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.

Nucleus0.668

Rank 1 · TkA07G077740 · TK1151

Cytoplasm0.290

Rank 2 · TkA07G077740 · TK1151

Cell membrane0.073

Rank 3 · TkA07G077740 · TK1151

Endoplasmic reticulum0.055

Rank 4 · TkA07G077740 · TK1151

Mitochondrion0.048

Rank 5 · TkA07G077740 · 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.

PF04997RNA_pol_Rpb1_148-289 aa

PF04983RNA_pol_Rpb1_375-115 aa

PF19411Clink305-334 aa

PF00623RNA_pol_Rpb1_2324-477 aa

PF04983RNA_pol_Rpb1_3482-626 aa

PF03945Endotoxin_N582-652 aa

PF04998RNA_pol_Rpb1_5754-1173 aa

PF19411Clink879-913 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G077740	`PF04997`	RNA_pol_Rpb1_1	48	289	5.5e-14	52.9
TkA07G077740	`PF04983`	RNA_pol_Rpb1_3	75	115	3e-06	27.9
TkA07G077740	`PF19411`	Clink	305	334	0.25	12.1
TkA07G077740	`PF00623`	RNA_pol_Rpb1_2	324	477	1e-35	124.2
TkA07G077740	`PF04983`	RNA_pol_Rpb1_3	482	626	3e-06	27.9
TkA07G077740	`PF03945`	Endotoxin_N	582	652	1.2	9.5
TkA07G077740	`PF04998`	RNA_pol_Rpb1_5	754	1173	3.7e-11	43.7
TkA07G077740	`PF19411`	Clink	879	913	0.25	12.1
TkA07G077740	`PF04997`	RNA_pol_Rpb1_1	893	998	5.5e-14	52.9
TkA07G077740	`PF03945`	Endotoxin_N	912	976	1.2	9.5
TkA07G077740	`PF03945`	Endotoxin_N	1146	1177	1.2	9.5
TkA07G077740	`PF13634`	Nucleoporin_FG	1304	1386	0.053	15.1
TkA07G077740	`PF13634`	Nucleoporin_FG	1412	1478	0.053	15.1
TkA07G077740	`PF13634`	Nucleoporin_FG	1476	1546	0.053	15.1
TkA07G077740	`PF13634`	Nucleoporin_FG	1564	1629	0.053	15.1
TkA07G077740	`PF11523`	DUF3223	1734	1808	6.4e-27	94.6

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
`Q5D869`	Arabidopsis thaliana	sp\|Q5D869\|NRPE1_ARATH DNA-directed RNA polymerase V subunit 1	51.800%	Swiss-Prot	High
`Q9LQ02`	Arabidopsis thaliana	sp\|Q9LQ02\|NRPD1_ARATH DNA-directed RNA polymerase IV subunit 1	26.500%	Swiss-Prot	Low
`P18616`	Arabidopsis thaliana	sp\|P18616\|NRPB1_ARATH DNA-directed RNA polymerase II subunit RPB1	24.000%	Swiss-Prot	Low

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