TkA04G273860 | RubberDandelionOmics

Gene overview

TkA04G273860

Reference: TK1151 Chr: Chr04 Coordinates: 69182440-69192995 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2100 bp · TkA04G273860|TK1151|cDNA

ATGAAACTGTTGCATCAACCACATTCGGGATCAAATCAGGTGCTACTCAGACCACCCATTCATCTGCACCTTCGCCTTCTATTCCCTAATTTGGATGAAAGTGTTCTTAACCCAAAAAGCGGTTTATTTCCCGGACCTGATTCTAAAGCTGCTGATGTTGTTGCTAATCCTGAAGATGAAGAGAAGGAGCTAGAACATTGTTCTTTACAAGAAAAACTTGACAATGAGCTCAAAGAACTGGACAAATCTTCAAAACAAGA...

CDS

Download CDS FASTA

2100 bp · TkA04G273860|TK1151|CDS

ATGAAACTGTTGCATCAACCACATTCGGGATCAAATCAGGTGCTACTCAGACCACCCATTCATCTGCACCTTCGCCTTCTATTCCCTAATTTGGATGAAAGTGTTCTTAACCCAAAAAGCGGTTTATTTCCCGGACCTGATTCTAAAGCTGCTGATGTTGTTGCTAATCCTGAAGATGAAGAGAAGGAGCTAGAACATTGTTCTTTACAAGAAAAACTTGACAATGAGCTCAAAGAACTGGACAAATCTTCAAAACAAGA...

Protein

Download Protein FASTA

699 aa · TkA04G273860|TK1151|PROTEIN

MKLLHQPHSGSNQVLLRPPIHLHLRLLFPNLDESVLNPKSGLFPGPDSKAADVVANPEDEEKELEHCSLQEKLDNELKELDKSSKQERISILSCITQKPKFSIGYPSVSSQQLWKCTGYVPKKFNSQYREFPCVIHSVNQKKDDLNVVKDQNRKKMPKMDSQPHGDEGTGGGGGGGSPQKLTTNNALSYLKLVKDMFHDQREKYKMFLDVMKDFKAQRETGEIWPLAPHADRDLESGEINEDDKTTMKLQKDHKRVSENR...

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	`TkA04G273860`
TK1151 ID	TkA04G273860
OH-1004 ID	LXL04_034928
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	91.700
Protein coverage (%)	TK1151 98.856 / OH-1004 81.787 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 TkA04G273860

Location Chr04:69182440-69192995 (+)

Description Similar to BIG: Auxin transport protein BIG

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g02260`	Required for auxin efflux and polar auxin transport (PAT) influencing auxin-mediated developmental responses (e.g. cell elongation, apical dominance, lateral root production, inflorescence architecture, general growth and development).	BIG: a calossin-like protein required for polar auxin transport in Arabidopsis.2001 · DOI: 10.1101/gad.905201 Mutations in the huge Arabidopsis gene BIG affect a range of hormone and light responses.2003 · DOI: 10.1046/j.1365-313x.2003.01779.x The auxin transport inhibitor response 3 (tir3) allele of BIG and auxin transport inhibitors affect the gibberellin status of Arabidopsis.2005 · DOI: 10.1111/j.1365-313x.2004.02287.x CRM1/BIG-mediated auxin action regulates Arabidopsis inflorescence development.2007 · DOI: 10.1093/pcp/pcm094 Arabidopsis mutants define downstream branches in the phototransduction pathway.1994 · DOI: 10.1101/gad.8.3.339 Reduced naphthylphthalamic acid binding in the tir3 mutant of Arabidopsis is associated with a reduction in polar auxin transport and diverse morphological defects.1997 · DOI: 10.1105/tpc.9.5.745
`At3g01320`	Acts as a transcriptional repressor.	PAH-domain-specific interactions of the Arabidopsis transcription coregulator SIN3-LIKE1 (SNL1) with telomere-binding protein 1 and ALWAYS EARLY2 Myb-DNA binding factors.2010 · DOI: 10.1016/j.jmb.2009.11.065
`At1g70060`	Acts as a transcriptional repressor.	No verified direct reference in this release
`At5g15020`	Acts as a transcriptional repressor.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0247700`	Required for auxin efflux and polar auxin transport (PAT) influencing auxin-mediated developmental responses (e.g. cell elongation, apical dominance, lateral root production, inflorescence architecture, general growth and development) (By similarity).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_034928 · 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:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009620 response to fungus Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0009926 auxin polar transport Biological Process

GO:0010311 lateral root formation Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0048281 inflorescence morphogenesis Biological Process

KEGG gene cross-reference

ath:AT1G24190

ath:AT1G70060

ath:AT3G01320

ath:AT3G02260

dosa:Os09g0247700

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.

Nucleus0.636

Rank 1 · TkA04G273860 · TK1151

Cytoplasm0.286

Rank 2 · TkA04G273860 · TK1151

Cell membrane0.120

Rank 3 · TkA04G273860 · TK1151

Endoplasmic reticulum0.075

Rank 4 · TkA04G273860 · TK1151

Mitochondrion0.043

Rank 5 · TkA04G273860 · 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.

PF06156YabA59-85 aa

PF02671PAH202-218 aa

PF06156YabA240-291 aa

PF07650KH_2380-407 aa

PF00013KH_1383-410 aa

PF00249Myb_DNA-binding443-460 aa

PF30837UBR4_Ub460-475 aa

PF06156YabA602-639 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G273860	`PF06156`	YabA	59	85	6.8	8.1
TkA04G273860	`PF02671`	PAH	202	218	0.0047	17.3
TkA04G273860	`PF06156`	YabA	240	291	6.8	8.1
TkA04G273860	`PF07650`	KH_2	380	407	0.068	13.7
TkA04G273860	`PF00013`	KH_1	383	410	0.0002	21.8
TkA04G273860	`PF00249`	Myb_DNA-binding	443	460	0.0022	18.8
TkA04G273860	`PF30837`	UBR4_Ub	460	475	2.8e-07	31.1
TkA04G273860	`PF06156`	YabA	602	639	6.8	8.1
TkA04G273860	`PF30837`	UBR4_Ub	614	623	2.8e-07	31.1
TkA04G273860	`PF30837`	UBR4_Ub	671	698	2.8e-07	31.1

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
`Q9SRU2`	Arabidopsis thaliana	sp\|Q9SRU2\|BIG_ARATH Auxin transport protein BIG	92.100%	Swiss-Prot	Low
`Q9SRH9`	Arabidopsis thaliana	sp\|Q9SRH9\|SNL1_ARATH Paired amphipathic helix protein Sin3-like 1	73.900%	Swiss-Prot	Low
`O04539`	Arabidopsis thaliana	sp\|O04539\|SNL4_ARATH Paired amphipathic helix protein Sin3-like 4	73.800%	Swiss-Prot	Low
`Q9LFQ3`	Arabidopsis thaliana	sp\|Q9LFQ3\|SNL2_ARATH Paired amphipathic helix protein Sin3-like 2	75.000%	Swiss-Prot	Low
`B9G2A8`	Oryza sativa subsp. japonica	sp\|B9G2A8\|BIG_ORYSJ Auxin transport protein BIG	91.900%	Swiss-Prot	Low

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