TkA07G358770 | RubberDandelionOmics

Gene overview

TkA07G358770

Reference: TK1151 Chr: Chr07 Coordinates: 89887856-89891551 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2638 bp · TkA07G358770|TK1151|cDNA

TGTTTTGGGGAAGATTCATTGCAAACCCTTCTCCCCCTTCTCTCTCTATCGTGTTTTTCTTGTCCTCTCTCTCCACAGACTTCCACCATTCACGGACCCCACAATTCCTCTAAACCCCTTCTTCTCCCCCTTCCTTCTCTCTTCTCCTTTCTCTCTCTCGCTGCAATAATGCCAGCCTCCTCCTCAGAGACAAGGAACAGGTGGAGGAAACGGAAGCGAGGAGAGCAGTCCCGAAAACCTAGACCCCACGACGAAGACGA...

CDS

Download CDS FASTA

2400 bp · TkA07G358770|TK1151|CDS

TGTTTTGGGGAAGATTCATTGCAAACCCTTCTCCCCCTTCTCTCTCTATCGTGTTTTTCTTGTCCTCTCTCTCCACAGACTTCCACCATTCACGGACCCCACAATTCCTCTAAACCCCTTCTTCTCCCCCTTCCTTCTCTCTTCTCCTTTCTCTCTCTCGCTGCAATAATGCCAGCCTCCTCCTCAGAGACAAGGAACAGGTGGAGGAAACGGAAGCGAGGAGAGCAGTCCCGAAAACCTAGACCCCACGACGAAGACGA...

Protein

Download Protein FASTA

799 aa · TkA07G358770|TK1151|PROTEIN

CFGEDSLQTLLPLLSLSCFSCPLSPQTSTIHGPHNSSKPLLLPLPSLFSFLSLAAIMPASSSETRNRWRKRKRGEQSRKPRPHDEDDEDYEEEDDVDLDQQNSHPEFDDGPSNSPDPTAATGAETEVISDGAVRISTFPSVIKHTVNQHHYSVIQSVARERACRTGDSSNGGLNYVFLENISHGQLQALSAMPKDAPALTGGDSEGSFVITPPPIMEGRGVVKRYGLDRVHVVPMHADWFSPTTVNRLERQAVPHFFSGK...

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	`TkA07G358770`
TK1151 ID	TkA07G358770
OH-1004 ID	LXL04_029908
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.700
Protein coverage (%)	TK1151 99.249 / 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA07G358770

Location Chr07:89887856-89891551 (+)

Description Similar to SWI3C: SWI/SNF complex subunit SWI3C

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g21700`	Component of a multiprotein complex equivalent of the SWI/SNF complex, an ATP-dependent chromatin-remodeling complex, which is required for the positive and negative regulation of gene expression of a large number of genes.	CHB2, a member of the SWI3 gene family, is a global regulator in Arabidopsis.2003 · DOI: 10.1023/b:plan.0000004305.60407.8b SWI3 subunits of putative SWI/SNF chromatin-remodeling complexes play distinct roles during Arabidopsis development.2005 · DOI: 10.1105/tpc.105.031203
`At4g34430`	Component of a multiprotein complex equivalent of the SWI/SNF complex, an ATP-dependent chromatin-remodeling complex, which is required for the positive and negative regulation of gene expression of a large number of genes.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os11g0183700`	Component of a multiprotein complex equivalent of the SWI/SNF complex, an ATP-dependent chromatin-remodeling complex, which is required for the positive and negative regulation of gene expression of a large number of genes.	A lamin-like protein OsNMCP1 regulates drought resistance and root growth through chromatin accessibility modulation by interacting with a chromatin remodeller OsSWI3C in rice.2020 · DOI: 10.1111/nph.16518

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029908 · 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:0006325 chromatin organization Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

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

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0045815 transcription initiation-coupled chromatin remodeling Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:2000070 regulation of response to water deprivation Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G21700

ath:AT2G47620

ath:AT4G34430

dosa:Os11g0183700

spo:2541851

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.

Nucleus0.945

Rank 1 · TkA07G358770 · TK1151

Cytoplasm0.101

Rank 2 · TkA07G358770 · TK1151

Cell membrane0.031

Rank 3 · TkA07G358770 · TK1151

Plastid0.017

Rank 4 · TkA07G358770 · TK1151

Endoplasmic reticulum0.016

Rank 5 · TkA07G358770 · 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.

PF13921Myb_DNA-bind_653-72 aa

PF00249Myb_DNA-binding65-71 aa

PF23048SH3-A_UBE2O85-148 aa

PF04433SWIRM241-320 aa

PF16282SANT_DAMP1_like453-486 aa

PF00249Myb_DNA-binding457-497 aa

PF13921Myb_DNA-bind_6458-499 aa

PF23048SH3-A_UBE2O584-605 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G358770	`PF13921`	Myb_DNA-bind_6	53	72	1e-06	29.5
TkA07G358770	`PF00249`	Myb_DNA-binding	65	71	1e-09	39.1
TkA07G358770	`PF23048`	SH3-A_UBE2O	85	148	7.2	8.1
TkA07G358770	`PF04433`	SWIRM	241	320	2.7e-21	76.3
TkA07G358770	`PF16282`	SANT_DAMP1_like	453	486	0.13	13.2
TkA07G358770	`PF00249`	Myb_DNA-binding	457	497	1e-09	39.1
TkA07G358770	`PF13921`	Myb_DNA-bind_6	458	499	1e-06	29.5
TkA07G358770	`PF23048`	SH3-A_UBE2O	584	605	7.2	8.1
TkA07G358770	`PF16495`	SWIRM-assoc_1	636	710	3e-25	88.7

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
`Q9XI07`	Arabidopsis thaliana	sp\|Q9XI07\|SWI3C_ARATH SWI/SNF complex subunit SWI3C	48.900%	Swiss-Prot	Medium
`Q8VY05`	Arabidopsis thaliana	sp\|Q8VY05\|SWI3D_ARATH SWI/SNF complex subunit SWI3D	35.400%	Swiss-Prot	Low
`Q53KK6`	Oryza sativa subsp. japonica	sp\|Q53KK6\|SWI3C_ORYSJ SWI/SNF complex subunit SWI3C homolog	45.400%	Swiss-Prot	Medium

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