TkA06G063640 | RubberDandelionOmics

Gene overview

TkA06G063640

Reference: TK1151 Chr: Chr06 Coordinates: 17171299-17172498 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1140 bp · TkA06G063640|TK1151|cDNA

AAACTGTTGCTCTATATATAAGCGCGTGGGCGTGGGAAGAAACTTATCCCAAGTTTCTAGAGAGAGACTAGGGTTTGCTCTCTTGAGTTTGGGGTTTTTTGATTTCTAGGGTTTGTGAGGTTTTCTTCGATTCAAAAAATGGACGTTGACGGCGCAAGGAAATCAGGAACCGTCAAGTGGTTCAACGACACCAAGGGATTTGGTTTCATCACTCCTGAAGATGGCGGTGAGGAGCTTTTTGTTCACCAATCGTCCATCAG...

CDS

Download CDS FASTA

603 bp · TkA06G063640|TK1151|CDS

ATGGACGTTGACGGCGCAAGGAAATCAGGAACCGTCAAGTGGTTCAACGACACCAAGGGATTTGGTTTCATCACTCCTGAAGATGGCGGTGAGGAGCTTTTTGTTCACCAATCGTCCATCAGAACGGAGGGATTCCGCAGCCTTGGTGACGGTGAGACCGTTGAGTACGTGATTGAGAACGGATCTGATGGCCGTACTAAAGCAGCTGATGTTACCGGCCCCAATGAAGGTCCCGTCCAGGGGAGTACCCGTGGTGGTGA...

Protein

Download Protein FASTA

200 aa · TkA06G063640|TK1151|PROTEIN

MDVDGARKSGTVKWFNDTKGFGFITPEDGGEELFVHQSSIRTEGFRSLGDGETVEYVIENGSDGRTKAADVTGPNEGPVQGSTRGGDRYGGGGGGYNGGSRGGRGGGGYGGGGGGYGGGGGYGGGGGGGNACFKCGESGHMARECTQNGGGGGGGYGGRGGGGYGGGGGRGGGGGGGGGGCYNCGEDGHFARECPTSNNR

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	`TkA06G063640`
TK1151 ID	TkA06G063640
OH-1004 ID	LXL04_025331
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	83.200
Protein coverage (%)	TK1151 100.000 / OH-1004 70.740 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 TkA06G063640

Location Chr06:17171299-17172498 (-)

Description Similar to GRP-2: Glycine-rich protein 2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g21060`	Chaperone that binds to and unwinds RNA and both single-stranded DNA and double-stranded DNA (ssDNA and dsDNA DNA) (By similarity).	Arabidopsis cold shock domain proteins: relationships to floral and silique development.2009 · DOI: 10.1093/jxb/ern351 Overexpression of AtCSP4 affects late stages of embryo development in Arabidopsis.2011 · DOI: 10.1093/jxb/erq400
`At4g38680`	Chaperone that binds to RNA, single- (ssDNA) and double- stranded (dsDNA) DNA, and unwinds nucleic acid duplex.	Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli.2007 · DOI: 10.1093/nar/gkl1076 Arabidopsis COLD SHOCK DOMAIN PROTEIN2 is a RNA chaperone that is regulated by cold and developmental signals.2007 · DOI: 10.1016/j.bbrc.2007.10.059 Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions.2009 · DOI: 10.1093/pcp/pcp037 Arabidopsis cold shock domain proteins: relationships to floral and silique development.2009 · DOI: 10.1093/jxb/ern351
`At2g17870`	Chaperone that binds to RNA, single- (ssDNA) and double-stranded (dsDNA) DNA, and unwinds nucleic acid duplex.	Cold shock domain protein 3 regulates freezing tolerance in Arabidopsis thaliana.2009 · DOI: 10.1074/jbc.m109.025791
`At4g36020`	Chaperone that binds to RNA, single- (ssDNA) and double-stranded (dsDNA) DNA, and unwinds nucleic acid duplex.	Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli.2007 · DOI: 10.1093/nar/gkl1076 Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions.2009 · DOI: 10.1093/pcp/pcp037

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025331 · 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:0009409 response to cold Biological Process

GO:0009631 cold acclimation Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005829 cytosol Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0140691 RNA folding chaperone Molecular Function

KEGG gene cross-reference

ath:AT2G17870

ell:WFL_03370

elw:ECW_m0678

nsy:104218376

sfl:SF0657

sfx:S0680

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.

Cytoplasm0.649

Rank 1 · TkA06G063640 · TK1151

Nucleus0.627

Rank 2 · TkA06G063640 · TK1151

Extracellular0.152

Rank 3 · TkA06G063640 · TK1151

Endoplasmic reticulum0.060

Rank 4 · TkA06G063640 · TK1151

Cell membrane0.055

Rank 5 · TkA06G063640 · 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.

PF00313CSD9-73 aa

PF08206OB_RNB19-41 aa

PF13917zf-CCHC_3128-147 aa

PF30379SLU7_N128-145 aa

PF14787zf-CCHC_5130-146 aa

PF27939DUF8363130-147 aa

PF00098zf-CCHC131-147 aa

PF14392zf-CCHC_4131-146 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G063640	`PF00313`	CSD	9	73	1.6e-25	89.4
TkA06G063640	`PF08206`	OB_RNB	19	41	0.0012	19.2
TkA06G063640	`PF13917`	zf-CCHC_3	128	147	0.00031	21.2
TkA06G063640	`PF30379`	SLU7_N	128	145	0.53	10.5
TkA06G063640	`PF14787`	zf-CCHC_5	130	146	0.0029	18.0
TkA06G063640	`PF27939`	DUF8363	130	147	0.22	12.1
TkA06G063640	`PF00098`	zf-CCHC	131	147	1.9e-16	60.0
TkA06G063640	`PF14392`	zf-CCHC_4	131	146	0.37	11.2
TkA06G063640	`PF13696`	zf-CCHC_2	132	145	0.043	14.4
TkA06G063640	`PF30379`	SLU7_N	177	194	0.53	10.5
TkA06G063640	`PF00098`	zf-CCHC	180	195	1.9e-16	60.0
TkA06G063640	`PF13917`	zf-CCHC_3	180	195	0.00031	21.2
TkA06G063640	`PF14787`	zf-CCHC_5	180	194	0.0029	18.0
TkA06G063640	`PF13696`	zf-CCHC_2	181	196	0.043	14.4
TkA06G063640	`PF27939`	DUF8363	181	196	0.22	12.1
TkA06G063640	`PF14392`	zf-CCHC_4	181	195	0.37	11.2

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
`Q38896`	Arabidopsis thaliana	sp\|Q38896\|CSP4_ARATH Cold shock domain-containing protein 4	67.800%	Swiss-Prot	High
`Q41188`	Arabidopsis thaliana	sp\|Q41188\|CSP2_ARATH Cold shock protein 2	65.700%	Swiss-Prot	High
`Q94C69`	Arabidopsis thaliana	sp\|Q94C69\|CSP3_ARATH Cold shock domain-containing protein 3	65.800%	Swiss-Prot	Low
`O65639`	Arabidopsis thaliana	sp\|O65639\|CSP1_ARATH Cold shock protein 1	60.500%	Swiss-Prot	Low

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