TkA04G042670 | RubberDandelionOmics

Gene overview

TkA04G042670

Reference: TK1151 Chr: Chr04 Coordinates: 11446127-11450605 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2512 bp · TkA04G042670|TK1151|cDNA

TTGCGTTTTAGGTGGTTCCATTTCCATATAAGTGGATTCCCCACTCTTTCTTTCTCTCTCTATTTGCGTCTTCAATTTCTTCTTATCACCTTCAAACTCCAACACATATTCACGCTTTGACATTTTTTGACAGATCCGTTCACCCTTTCTACTCCTACAGATAATTATCAAGCTTAACATAGCAAATCTTCGATCAAACCATTTTGAAGAAGAAATCTCCACTTCATCAAGGAACACTTTCCTGCATGACATTTTGACAT...

CDS

Download CDS FASTA

1980 bp · TkA04G042670|TK1151|CDS

ATGTCAGGGTTGCTTAATAATTCATCTTTAAGTGGATCGGCTTCAAATCTTCAAGATAACACAGCCGGGAGACAATTTTCCACATCTTTCACTGCTCAATCTGGTGCACCTTCCCCTGGTTTCCCACACAGTGGATCTATTCAAGGCCTTCATAACCTACATGGCAGTTACAATGTTCCCAACATGCCAGGCACACTTGGATCAAGAAACTCAACAATGTCCAATGTCCCTTCAACTGGACTTCAACAACCAACTGGAAA...

Protein

Download Protein FASTA

659 aa · TkA04G042670|TK1151|PROTEIN

MSGLLNNSSLSGSASNLQDNTAGRQFSTSFTAQSGAPSPGFPHSGSIQGLHNLHGSYNVPNMPGTLGSRNSTMSNVPSTGLQQPTGNLSGRFSSNIPVALSQISHGNSHGHPGLSNRGGMGVVGGPGYTSSTNAVGGSIPGILPTSAAIGNRNSIPGVGVSPMLGNSGPRITNSSGNIVGGGNIGRTINSGGGGLSIPGLSSRLNLNTNSGSVNVNVQGSNRLMGGMLQQASPQVMSMLGNSYHSGGPLSQNHVQGVNSL...

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	`TkA04G042670`
TK1151 ID	TkA04G042670
OH-1004 ID	LXL04_036479
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.800
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 TkA04G042670

Location Chr04:11446127-11450605 (+)

Description Similar to VIP2: Probable NOT transcription complex subunit VIP2 (Fragment)

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g59710`	Transcriptional regulator required for Agrobacterium-mediated stable genetic transformation by T-DNA integration in host genome, but not for T-DNA transient expression.	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_036479 · 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:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0006417 regulation of translation Biological Process

GO:0010606 positive regulation of cytoplasmic mRNA processing body assembly Biological Process

GO:0015074 DNA integration Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0033147 negative regulation of intracellular estrogen receptor signaling pathway Biological Process

GO:2000036 regulation of stem cell population maintenance Biological Process

GO:0000932 P-body Cellular Component

KEGG gene cross-reference

ath:AT5G59710

hsa:4848

mmu:72068

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.

Cytoplasm0.721

Rank 1 · TkA04G042670 · TK1151

Nucleus0.273

Rank 2 · TkA04G042670 · TK1151

Lysosome / Vacuole0.058

Rank 3 · TkA04G042670 · TK1151

Cell membrane0.050

Rank 4 · TkA04G042670 · TK1151

Golgi apparatus0.043

Rank 5 · TkA04G042670 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF04153NOT2_3_5_C446-460 aa

PF04153NOT2_3_5_C528-649 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G042670	`PF04153`	NOT2_3_5_C	446	460	1.2e-37	129.5
TkA04G042670	`PF04153`	NOT2_3_5_C	528	649	1.2e-37	129.5

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
`Q9FPW4`	Arabidopsis thaliana	sp\|Q9FPW4\|VIP2_ARATH Probable NOT transcription complex subunit VIP2	60.200%	Swiss-Prot	High

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