TkA05G398720 | RubberDandelionOmics

Gene overview

TkA05G398720

Reference: TK1151 Chr: Chr05 Coordinates: 99123520-99131820 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1488 bp · TkA05G398720|TK1151|cDNA

AAAACACATAAAAACTCTTTATGTGATTTCTGTTGTTGGTCATAGACGCGCCACTCTTCAAACACGACGCGGCACACTTTCTTCTCCTCCTCTGTAAAAACTTATACCAACCGCCCTCCGCCCCCTTTCCAATTCCATCAACGCCATGTCTCAAGGAGTCCATAGCAGCGGCGACGGCGACGGCGGGGGAAGCACTCATGGTGCAATCCCTAAGTTATACTTCTGTTACCAGTGTGAACACACGGTCTCCATTACAACTT...

CDS

Download CDS FASTA

1566 bp · TkA05G398720|TK1151|CDS

ATGATCGGGAGATTAGGAGATGGACGCCACCATATCGCCACCATCACCAAGGACAGATTCCTAGGGTTTCTAATCTGGCAATCATTTCCTTCAACCCTCGTCTACCTTCTCTGCAAAACCCTGCTCGCCCCATTAGCCCCCGCCACCACCCTCGTCGCCGCCGTCTCCGCCTTCCTCTTCTTCCAGCTCTCCCTCCTTCTGTTCTCAACCTCTCTCTTCCTAGTCTCCTCTCCTCAACCCGTTCGTGGAGTTTCACCGAT...

Protein

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521 aa · TkA05G398720|TK1151|PROTEIN

MIGRLGDGRHHIATITKDRFLGFLIWQSFPSTLVYLLCKTLLAPLAPATTLVAAVSAFLFFQLSLLLFSTSLFLVSSPQPVRGVSPIELLLGLLKLIFVYGGQPLPSDFRRRARVTLSFILFLASSGVSAYLSVVCLSGSEVFGSLGLRGLAVGLMYGSHYVFTRRWVLDFPIVQRPLFFSYKMGIRKAIVKALKLSTPAYLLSLPLHIFVNDQKSLGDIIINQIVFYLSCAVIFLCWELNHHLLQVFLTKRYQFAPPKG...

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	`TkA05G398720`
TK1151 ID	TkA05G398720
OH-1004 ID	LXL04_011658
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	43.700
Protein coverage (%)	TK1151 94.434 / OH-1004 94.725 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 TkA05G398720

Location Chr05:99123520-99131820 (-)

Description Protein of unknown function

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g19950`	E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.	No verified direct reference in this release
`At3g56580`	E3 ubiquitin-protein ligase that promotes osmotic stress and abscisic acid (ABA) responses.	The atrzf1 mutation of the novel RING-type E3 ubiquitin ligase increases proline contents and enhances drought tolerance in Arabidopsis.2013 · DOI: 10.1016/j.plantsci.2012.12.007 PCA22 acts as a suppressor of atrzf1 to mediate proline accumulation in response to abiotic stress in Arabidopsis.2017 · DOI: 10.1093/jxb/erx069
`At2g40830`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0488800`	Possesses E3 ubiqutin-protein ligase activity in vitro.	Molecular dissection of Oryza sativa salt-induced RING Finger Protein 1 (OsSIRP1): possible involvement in the sensitivity response to salinity stress.2016 · DOI: 10.1111/ppl.12459

Functional annotation source

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Functional annotation source: OH1004 · LXL04_011658 · 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) No functional description available

KEGG gene cross-reference No functional description available

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

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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.

Endoplasmic reticulum0.536

Rank 1 · TkA05G398720 · TK1151

Nucleus0.260

Rank 2 · TkA05G398720 · TK1151

Golgi apparatus0.109

Rank 3 · TkA05G398720 · TK1151

Cytoplasm0.108

Rank 4 · TkA05G398720 · TK1151

Cell membrane0.089

Rank 5 · TkA05G398720 · 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.

PF09531Ndc1_Nup37-65 aa

PF09531Ndc1_Nup224-344 aa

PF19011DUF5740331-367 aa

PF09531Ndc1_Nup363-478 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA05G398720	`PF09531`	Ndc1_Nup	37	65	3.6e-09	36.6
TkA05G398720	`PF09531`	Ndc1_Nup	224	344	3.6e-09	36.6
TkA05G398720	`PF19011`	DUF5740	331	367	0.2	12.3
TkA05G398720	`PF09531`	Ndc1_Nup	363	478	3.6e-09	36.6

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8LPN7`	Arabidopsis thaliana	sp\|Q8LPN7\|RNG1L_ARATH E3 ubiquitin-protein ligase RING1-like	51.200%	Swiss-Prot	High
`Q94AK4`	Arabidopsis thaliana	sp\|Q94AK4\|RZF1_ARATH E3 ubiquitin-protein ligase RZF1	37.100%	Swiss-Prot	Medium
`O22197`	Arabidopsis thaliana	sp\|O22197\|RHC1A_ARATH Probable E3 ubiquitin-protein ligase RHC1A	32.300%	Swiss-Prot	Medium
`Q6AVN2`	Oryza sativa subsp. japonica	sp\|Q6AVN2\|SIRP1_ORYSJ E3 ubiquitin-protein ligase SIRP1	30.900%	Swiss-Prot	Medium

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