TkA06G094110 | RubberDandelionOmics

Gene overview

TkA06G094110

Reference: TK1151 Chr: Chr06 Coordinates: 24996456-24999539 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1578 bp · TkA06G094110|TK1151|cDNA

ATGGCCCAGGCCCAACAATCGCGGTGTGTTATTTATGCATCTCTGGCGCGTGGCAATAACAACTCAACCTTTTCCTCTTGCCTTGAGAAAGGGGGTATACCACCGTATACACCCCACACCTTCTCGCACACACACAGACGCACAGAAGACGAAATCGACGGCAAATTGAAAGATGAAGGTTTTTGTGAAAACATTGAGGGGACTCACTTCGAAATCGAAGTAAAACCCGAGGACACGGTTGCTGATGTGAAGAAAAATAT...

CDS

Download CDS FASTA

552 bp · TkA06G094110|TK1151|CDS

ATGGCCCAGGCCCAACAATCGCGGTGTGTTATTTATGCATCTCTGGCGCGTGGCAATAACAACTCAACCTTTTCCTCTTGCCTTGAGAAAGGGGGTATACCACCGTATACACCCCACACCTTCTCGCACACACACAGACGCACAGAAGACGAAATCGACGGCAAATTGAAAGATGAAGGTTTTTGTGAAAACATTGAGGGGACTCACTTCGAAATCGAAGTAAAACCCGAGGACACGGTTGCTGATGTGAAGAAAAATAT...

Protein

Download Protein FASTA

183 aa · TkA06G094110|TK1151|PROTEIN

MAQAQQSRCVIYASLARGNNNSTFSSCLEKGGIPPYTPHTFSHTHRRTEDEIDGKLKDEGFCENIEGTHFEIEVKPEDTVADVKKNIESVQGDVYPAALQMLIHQGKVLKDTTTLEENKVAENSFIVIMLSKNKVASGETSTTTAAQRHLRQVPPLLHQQPLKLRHLSHRLYLLLQLPIQHLL

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	`TkA06G094110`
TK1151 ID	TkA06G094110
OH-1004 ID	LXL04_024957
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	68.300
Protein coverage (%)	TK1151 80.874 / OH-1004 35.982 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 TkA06G094110

Location Chr06:24996456-24999539 (+)

Description Similar to RAD23D: Ubiquitin receptor RAD23d

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g02540`	May be involved in nucleotide excision repair (By similarity).	No verified direct reference in this release
`At5g38470`	May be involved in nucleotide excision repair (By similarity).	No verified direct reference in this release
`At1g16190`	May be involved in nucleotide excision repair (By similarity).	No verified direct reference in this release
`At1g79650`	May be involved in nucleotide excision repair (By similarity).	The RAD23 family provides an essential connection between the 26S proteasome and ubiquitylated proteins in Arabidopsis.2010 · DOI: 10.1105/tpc.109.072660 RAD4 and RAD23/HMR Contribute to Arabidopsis UV Tolerance.2017 · DOI: 10.3390/genes9010008

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0407200`	May be involved in nucleotide excision repair (By similarity).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_024957 · 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:0006289 nucleotide-excision repair Biological Process

GO:0009409 response to cold Biological Process

GO:0009411 response to UV Biological Process

GO:0009650 UV protection Biological Process

GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009536 plastid Cellular Component

GO:0003684 damaged DNA binding Molecular Function

GO:0031593 polyubiquitin modification-dependent protein binding Molecular Function

KEGG gene cross-reference

ath:AT1G16190

ath:AT1G79650

ath:AT3G02540

ath:AT5G38470

dosa:Os09g0407200

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.

Cytoplasm0.491

Rank 1 · TkA06G094110 · TK1151

Nucleus0.383

Rank 2 · TkA06G094110 · TK1151

Cell membrane0.119

Rank 3 · TkA06G094110 · TK1151

Mitochondrion0.112

Rank 4 · TkA06G094110 · TK1151

Endoplasmic reticulum0.100

Rank 5 · TkA06G094110 · 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.

PF00240ubiquitin65-132 aa

PF11976Rad60-SLD66-129 aa

PF13881Rad60-SLD_267-127 aa

PF20147Crinkler68-121 aa

PF10302Dsc3_N70-132 aa

PF21696TECR_N74-120 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G094110	`PF00240`	ubiquitin	65	132	3.2e-16	59.6
TkA06G094110	`PF11976`	Rad60-SLD	66	129	0.0028	18.2
TkA06G094110	`PF13881`	Rad60-SLD_2	67	127	0.01	16.7
TkA06G094110	`PF20147`	Crinkler	68	121	0.079	14.4
TkA06G094110	`PF10302`	Dsc3_N	70	132	0.00088	20.5
TkA06G094110	`PF21696`	TECR_N	74	120	0.0037	18.0

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
`Q84L31`	Arabidopsis thaliana	sp\|Q84L31\|RD23C_ARATH Ubiquitin receptor RAD23c	68.000%	Swiss-Prot	Medium
`Q84L30`	Arabidopsis thaliana	sp\|Q84L30\|RD23D_ARATH Ubiquitin receptor RAD23d	69.700%	Swiss-Prot	Low
`Q84L32`	Arabidopsis thaliana	sp\|Q84L32\|RD23A_ARATH Probable ubiquitin receptor RAD23a	58.000%	Swiss-Prot	Low
`Q84L33`	Arabidopsis thaliana	sp\|Q84L33\|RD23B_ARATH Ubiquitin receptor RAD23b	55.300%	Swiss-Prot	Low
`Q40742`	Oryza sativa subsp. japonica	sp\|Q40742\|RAD23_ORYSJ Probable ubiquitin receptor RAD23	55.400%	Swiss-Prot	Low

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