TkA06G480110 | RubberDandelionOmics

Gene overview

TkA06G480110

Reference: TK1151 Chr: Chr06 Coordinates: 118978829-118986010 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA No cDNA sequence available

cDNA

No cDNA sequence is available for this reference.

CDS

Download CDS FASTA

1122 bp · TkA06G480110|TK1151|CDS

ATGGAGGCAAAAAGTTCAGGGCGTATCATACCTCGTGATGGGGTTGATAAAGAATACGACATTGCTTGCACAATGGTTGCAGATATTGAGTCTAGTCTCGCAAAGCATTTAAAGGAACAAAGAAAGCTACTTGAAGATTCATCAATGAATTATGTTACAGTCGGAAAAGATATGTATCTTCTAGAAGTATCTGAAAGCTTGTCTGCAAGTGTTCCTTGTGACTATGAGCGAAGATCATCCAAAAAGGGTTGTGTGAGGTA...

Protein

Download Protein FASTA

373 aa · TkA06G480110|TK1151|PROTEIN

MEAKSSGRIIPRDGVDKEYDIACTMVADIESSLAKHLKEQRKLLEDSSMNYVTVGKDMYLLEVSESLSASVPCDYERRSSKKGCVRYWTPEIKHYIRELSEAESEKESKLKSIMQRLIGRFCEHHVSWRQLVSTVAELDVLISISIASDMYEGPTCRPLIVDSDEAPVVSAKNLGHPVLRNGSLGDGSGTAFVPNDVCIDDDARFIVLTGPNMGGKSTLLRQVCLAVIIAQVGADVPAESFKMSPVDRIFVRMGAKDHIM...

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	`TkA06G480110`
TK1151 ID	TkA06G480110
OH-1004 ID	LXL04_022524
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.700
Protein coverage (%)	TK1151 94.906 / OH-1004 39.073 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA06G480110

Location Chr06:118978829-118986010 (+)

Description Similar to MSH6: DNA mismatch repair protein MSH6

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g02070`	Component of the post-replicative DNA mismatch repair system (MMR).	Arabidopsis MutS homologs-AtMSH2, AtMSH3, AtMSH6, and a novel AtMSH7-form three distinct protein heterodimers with different specificities for mismatched DNA.2000 · DOI: 10.1105/tpc.12.6.991 Dissimilar mispair-recognition spectra of Arabidopsis DNA-mismatch-repair proteins MSH2MSH6 (MutSalpha) and MSH2MSH7 (MutSgamma).2003 · DOI: 10.1093/nar/gkg780 Regulation of plant MSH2 and MSH6 genes in the UV-B-induced DNA damage response.2011 · DOI: 10.1093/jxb/err001

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_022524 · 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:0000710 meiotic mismatch repair Biological Process

GO:0006281 DNA repair Biological Process

GO:0006290 pyrimidine dimer repair Biological Process

GO:0006298 mismatch repair Biological Process

GO:0007095 mitotic G2 DNA damage checkpoint signaling Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0008340 determination of adult lifespan Biological Process

GO:0009411 response to UV Biological Process

GO:0032876 negative regulation of DNA endoreduplication Biological Process

GO:0045910 negative regulation of DNA recombination Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT4G02070

dme:Dmel_CG7003

hsa:2956

mmu:17688

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.626

Rank 1 · TkA06G480110 · TK1151

Cytoplasm0.480

Rank 2 · TkA06G480110 · TK1151

Cell membrane0.050

Rank 3 · TkA06G480110 · TK1151

Mitochondrion0.040

Rank 4 · TkA06G480110 · TK1151

Endoplasmic reticulum0.035

Rank 5 · TkA06G480110 · 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.

PF05190MutS_IV14-104 aa

PF05192MutS_III45-144 aa

PF28561RRG1_C52-120 aa

PF12612TFCD_C85-154 aa

PF12616DUF377591-137 aa

PF13173AAA_14103-121 aa

PF25199nSTAND_NTPase5201-228 aa

PF13401AAA_22201-290 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G480110	`PF05190`	MutS_IV	14	104	1.9e-17	64.0
TkA06G480110	`PF05192`	MutS_III	45	144	2.7e-05	25.3
TkA06G480110	`PF28561`	RRG1_C	52	120	0.29	11.7
TkA06G480110	`PF12612`	TFCD_C	85	154	0.069	13.7
TkA06G480110	`PF12616`	DUF3775	91	137	0.066	13.8
TkA06G480110	`PF13173`	AAA_14	103	121	0.29	11.8
TkA06G480110	`PF25199`	nSTAND_NTPase5	201	228	0.025	15.1
TkA06G480110	`PF13401`	AAA_22	201	290	0.16	13.0
TkA06G480110	`PF13173`	AAA_14	204	228	0.29	11.8
TkA06G480110	`PF00488`	MutS_V	206	347	5.1e-56	190.3
TkA06G480110	`PF12616`	DUF3775	269	298	0.066	13.8

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
`O04716`	Arabidopsis thaliana	sp\|O04716\|MSH6_ARATH DNA mismatch repair protein MSH6	72.600%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card