TkA01G588260 | RubberDandelionOmics

Gene overview

TkA01G588260

Reference: TK1151 Chr: Chr01 Coordinates: 147978358-147980720 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1377 bp · TkA01G588260|TK1151|cDNA

ATTTAGCGTACCACTATTTATACAAACTTTATTTTTCATTGTTAACACAACAATCGTCAACAAATCCTCTAAAGAAACCTTGACATCGAGAGCACATCCTTAACGCAAAGGTAATAGAAGGTATCTACCTCAAAATTTCACCATCAACCCGTTTGATTCGACTTGTGGGTGAAGTCCGCAAAAACTAGGGTTTTTGATATTACTGGGTTTGGAGGGATCCAAGGAGCATACTGAGAGAAGAGGAAGATGACGACTAGAAT...

CDS

Download CDS FASTA

1062 bp · TkA01G588260|TK1151|CDS

ATGACGACTAGAATAGCTCCAGGCGTCGGGGCGAACCTGCTAGGTCAACACTCGGCGGAGAGGAACCAAGACGCCACTGCCTACGTCGGCAATCTTGACCCTCAGGCATCCGAAGAGCTATTATGGGAGTTGTTTGTTCAAGCTGGCCCAGTTGTGAACGTGTATGTTCCTAAAGATAGAGTCACCAATCTCCACCAAGGCTATGGATTTGTAGAGTTCCGAAGTGAAGAAGATGCTGATTATGCAATTAAAGTTCTCAA...

Protein

Download Protein FASTA

353 aa · TkA01G588260|TK1151|PROTEIN

MTTRIAPGVGANLLGQHSAERNQDATAYVGNLDPQASEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLNMIKLYGKPIRVNKASQDKKSLDVGANLFVGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIESMNGQYLCNRQITVSYAYKKDTKGERHGTPAERTLASSNPTTQKSRPHTLFASGPPTLAQPNGAPRPFVNGALPPVQTIPAIRPAPPP...

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	`TkA01G588260`
TK1151 ID	TkA01G588260
OH-1004 ID	LXL04_000787
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	100.000
Protein coverage (%)	TK1151 76.487 / OH-1004 76.487 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	`TkA01G588260`
Location	Chr01:147978358-147980720 (-)
Description	Similar to Sf3b4: Splicing factor 3B subunit 4
Arabidopsis / Rice Reference Genes and Papers	Download references for this gene Arabidopsis No hit for this species in the current source table. Rice No hit for this species in the current source table.
Functional annotation source	View annotation sources Functional annotation source: OH1004 · `LXL04_000787` · 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:0000375 RNA splicing, via transesterification reactions Biological Process GO:0000387 spliceosomal snRNP assembly Biological Process GO:0000388 spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) Biological Process GO:0000398 mRNA splicing, via spliceosome Biological Process GO:0006397 mRNA processing Biological Process GO:0008380 RNA splicing Biological Process GO:1903241 U2-type prespliceosome assembly Biological Process GO:0005634 nucleus Cellular Component GO:0005654 nucleoplasm Cellular Component GO:0005681 spliceosomal complex Cellular Component GO:0005684 U2-type spliceosomal complex Cellular Component GO:0005686 U2 snRNP Cellular Component
KEGG gene cross-reference	hsa:10262 mmu:107701 rno:295270 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.

Nucleus0.571

Rank 1 · TkA01G588260 · TK1151

Cytoplasm0.565

Rank 2 · TkA01G588260 · TK1151

Cell membrane0.038

Rank 3 · TkA01G588260 · TK1151

Endoplasmic reticulum0.033

Rank 4 · TkA01G588260 · TK1151

Mitochondrion0.023

Rank 5 · TkA01G588260 · 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.

PF13893RRM_524-104 aa

PF00076RRM_128-97 aa

PF16367RRM_728-77 aa

PF22976RRM_1031-91 aa

PF08206OB_RNB65-88 aa

PF29326RRM_MUD2_C67-94 aa

PF25381PH_2681-108 aa

PF16367RRM_7113-172 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G588260	`PF13893`	RRM_5	24	104	0.015	15.7
TkA01G588260	`PF00076`	RRM_1	28	97	4.1e-43	145.8
TkA01G588260	`PF16367`	RRM_7	28	77	5.9e-06	26.9
TkA01G588260	`PF22976`	RRM_10	31	91	0.06	14.2
TkA01G588260	`PF08206`	OB_RNB	65	88	0.0011	19.3
TkA01G588260	`PF29326`	RRM_MUD2_C	67	94	0.0086	16.8
TkA01G588260	`PF25381`	PH_26	81	108	0.12	12.8
TkA01G588260	`PF16367`	RRM_7	113	172	5.9e-06	26.9
TkA01G588260	`PF13893`	RRM_5	113	188	0.015	15.7
TkA01G588260	`PF00076`	RRM_1	114	185	4.1e-43	145.8
TkA01G588260	`PF22976`	RRM_10	118	190	0.06	14.2
TkA01G588260	`PF08206`	OB_RNB	151	173	0.0011	19.3
TkA01G588260	`PF29326`	RRM_MUD2_C	157	193	0.0086	16.8

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.

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