TkA01G627160 | RubberDandelionOmics

Gene overview

TkA01G627160

Reference: TK1151 Chr: Chr01 Coordinates: 158339709-158342914 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2650 bp · TkA01G627160|TK1151|cDNA

AAACAACAAAAATTCAAACAATAGTCGGTCTGCCTAAAACCCTCGCTGCCTCGCCCACAGAAACTGTATTTTCCAGAAACAAGGGGATGAGTTTTGATCGATTACTGCTCGCTTCCATCGAAGATGAAGACCAAGATTTCGAGGAATCATCGTCGTCTACTCCGGCAACCCAGTCTGAAACCTTTATGGTGGGTTTCATAGTCGCCAACATTGTCGGTCTACAATACTATCGCGGCCGAATAAGCGGTCGAGAAATGGTT...

CDS

Download CDS FASTA

2175 bp · TkA01G627160|TK1151|CDS

ATGAGTTTTGATCGATTACTGCTCGCTTCCATCGAAGATGAAGACCAAGATTTCGAGGAATCATCGTCGTCTACTCCGGCAACCCAGTCTGAAACCTTTATGGTGGGTTTCATAGTCGCCAACATTGTCGGTCTACAATACTATCGCGGCCGAATAAGCGGTCGAGAAATGGTTGGTCTTGTCAGAGAACCCTTGAATGCCTACAACTCTAACGCCATCAAAGTCGTCAATACTCGAACTATTCAAGTTGGTCATATCGA...

Protein

Download Protein FASTA

724 aa · TkA01G627160|TK1151|PROTEIN

MSFDRLLLASIEDEDQDFEESSSSTPATQSETFMVGFIVANIVGLQYYRGRISGREMVGLVREPLNAYNSNAIKVVNTRTIQVGHIEKKVASVLAPLLDSNLVHVEGIVPKTPKSAAAYRIPCHIHVFSKMEAFETVKSALRSFLFTPNDPMFSMSDSMVVKEKKKGDLDEIFKLIDDNLRENAVNGVMEPPQDFILPDLFQHQKEGLYWLHHRENSDELPPFWEKSDDGFTNVLTNYQSDIRPEPLRGGIFADDMGLGK...

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	`TkA01G627160`
TK1151 ID	TkA01G627160
OH-1004 ID	LXL04_000221
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	94.400
Protein coverage (%)	TK1151 73.066 / OH-1004 61.290 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 TkA01G627160

Location Chr01:158339709-158342914 (+)

Description Similar to At5g05130: Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3-like 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g05130`	Possesses intrinsic ATP-dependent nucleosome-remodeling activity.	No verified direct reference in this release
`At5g22750`	Functions in error-free postreplication DNA repair or DNA- damage tolerance (DTT) pathway.	A homolog of ScRAD5 is involved in DNA repair and homologous recombination in Arabidopsis.2008 · DOI: 10.1104/pp.108.116806 RAD5A, RECQ4A, and MUS81 have specific functions in homologous recombination and define different pathways of DNA repair in Arabidopsis thaliana.2010 · DOI: 10.1105/tpc.110.078568 RAD5a and REV3 function in two alternative pathways of DNA-damage tolerance in Arabidopsis.2011 · DOI: 10.1016/j.dnarep.2011.04.009 AtRAD5A is a DNA translocase harboring a HIRAN domain which confers binding to branched DNA structures and is required for DNA repair in vivo.2016 · DOI: 10.1111/tpj.13283

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000221 · 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:0000209 protein polyubiquitination Biological Process

GO:0006281 DNA repair Biological Process

GO:0006325 chromatin organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006974 DNA damage response Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0042789 mRNA transcription by RNA polymerase II Biological Process

GO:0045944 positive regulation of transcription by RNA polymerase II Biological Process

GO:0070534 protein K63-linked ubiquitination Biological Process

GO:0071168 protein localization to chromatin Biological Process

GO:0071932 replication fork reversal Biological Process

GO:0141119 chromosomal DNA methylation maintenance following DNA replication Biological Process

KEGG gene cross-reference

ath:AT5G05130

hsa:6596

mmu:20585

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.

Nucleus0.714

Rank 1 · TkA01G627160 · TK1151

Cytoplasm0.251

Rank 2 · TkA01G627160 · TK1151

Mitochondrion0.047

Rank 3 · TkA01G627160 · TK1151

Cell membrane0.046

Rank 4 · TkA01G627160 · TK1151

Endoplasmic reticulum0.032

Rank 5 · TkA01G627160 · 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.

PF08797HIRAN36-129 aa

PF00176SNF2-rel_dom203-514 aa

PF04851ResIII248-432 aa

PF00270DEAD256-430 aa

PF18766SWI2_SNF2350-435 aa

PF18276TcA_TcB_BD479-536 aa

PF18276TcA_TcB_BD660-693 aa

PF18766SWI2_SNF2669-703 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G627160	`PF08797`	HIRAN	36	129	1.2e-20	73.9
TkA01G627160	`PF00176`	SNF2-rel_dom	203	514	1.9e-65	221.5
TkA01G627160	`PF04851`	ResIII	248	432	3.9e-06	27.6
TkA01G627160	`PF00270`	DEAD	256	430	5.3e-06	27.0
TkA01G627160	`PF18766`	SWI2_SNF2	350	435	0.07	13.5
TkA01G627160	`PF18276`	TcA_TcB_BD	479	536	0.06	13.1
TkA01G627160	`PF18276`	TcA_TcB_BD	660	693	0.06	13.1
TkA01G627160	`PF18766`	SWI2_SNF2	669	703	0.07	13.5
TkA01G627160	`PF18570`	Nup54_57_C	688	700	0.083	13.2

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
`Q9FF61`	Arabidopsis thaliana	sp\|Q9FF61\|SM3L1_ARATH Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3-like 1	59.800%	Swiss-Prot	High
`Q9FNI6`	Arabidopsis thaliana	sp\|Q9FNI6\|SM3L2_ARATH DNA repair protein RAD5A	34.900%	Swiss-Prot	Medium

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