TkA05G416600 | RubberDandelionOmics

Gene overview

TkA05G416600

Reference: TK1151 Chr: Chr05 Coordinates: 103680315-103690638 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4770 bp · TkA05G416600|TK1151|cDNA

GCTATGTTGACCTTTCAAAAACGAGTGGTAAACATATTATCCGTCAATAATCACAAAGAACAAATTTTAGCTGCAGTGAAATAGAACTACATCTGGTTCTTCCCTGCCCAAAGTCGCAGGGAGGTTTAAGCTCTTAAAACCCTAGTCACATACTGCTGAATCCTCCCTCTCTCTTGCTCTCCCAAAGCAATCCTACATTTCACGAATCATCGTTGAGAAATCTAATTACAAAGACGAAATGAGCTACGCAGCATACAAAT...

CDS

Download CDS FASTA

4317 bp · TkA05G416600|TK1151|CDS

ATGAGCTACGCAGCATACAAATTGATGCACCCGCCCACCGGAATCGACAACTGCGCATCAGGATTCATCACGCATTCTCCCGCCGACTTCGCTTCCCGCATTCTCCCAGCTCCTACTGATGAGATCGACCCCGTATGGCCCTCCGCCCCGACTCCAGGCGTCGGCCCTATCCCAAACCTCATCGTGACTGCAGCAAACGTTCTTGAAGTATACACAGTTAGGGTTCAGGAGGACGGTAATAGTACTAGTAAGGATTCTAG...

Protein

Download Protein FASTA

1438 aa · TkA05G416600|TK1151|PROTEIN

MSYAAYKLMHPPTGIDNCASGFITHSPADFASRILPAPTDEIDPVWPSAPTPGVGPIPNLIVTAANVLEVYTVRVQEDGNSTSKDSSTVAQPQRGGVMAGLSGASLELVCSYRLHGNVESVGVLSSGAEERTSGRRRDSIILTFEDAKISILEFDDSVYGLRTSSMHCFEGPQWLHLKKGRESFARGPFIKADPLGRCAGVLVYGLQMIILKAAEAGGLVGDDGGSSGGGSLSARAQSSYMISLRELDVKHVKDFIFVHG...

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	`TkA05G416600`
TK1151 ID	TkA05G416600
OH-1004 ID	LXL04_021704
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.200
Protein coverage (%)	TK1151 100.000 / OH-1004 96.463 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

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Basic Information and Functional Annotation

Gene ID TkA05G416600

Location Chr05:103680315-103690638 (-)

Description Similar to CPSF160: Cleavage and polyadenylation specificity factor subunit 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g51660`	CPSF plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A)polymerase and other factors to bring about cleavage and poly(A) addition.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0252200`	CPSF plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A)polymerase and other factors to bring about cleavage and poly(A) addition.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021704 · 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:0006397 mRNA processing Biological Process

GO:0031123 RNA 3'-end processing Biological Process

GO:0031124 mRNA 3'-end processing Biological Process

GO:0180012 co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005847 mRNA cleavage and polyadenylation specificity factor complex Cellular Component

GO:0003676 nucleic acid binding Molecular Function

GO:0003723 RNA binding Molecular Function

GO:0019899 enzyme binding Molecular Function

GO:0035925 mRNA 3'-UTR AU-rich region binding Molecular Function

KEGG gene cross-reference

ath:AT5G51660

bta:282703

hsa:29894

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.

Nucleus0.796

Rank 1 · TkA05G416600 · TK1151

Cytoplasm0.225

Rank 2 · TkA05G416600 · TK1151

Lysosome / Vacuole0.047

Rank 3 · TkA05G416600 · TK1151

Golgi apparatus0.044

Rank 4 · TkA05G416600 · TK1151

Cell membrane0.031

Rank 5 · TkA05G416600 · 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.

PF10433Beta-prop_RSE1_1st105-447 aa

PF23726Beta-prop_RSE1_2nd380-412 aa

PF23726Beta-prop_RSE1_2nd563-995 aa

PF03178CPSF_A1072-1402 aa

PF23726Beta-prop_RSE1_2nd1133-1383 aa

PF10433Beta-prop_RSE1_1st1150-1241 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA05G416600	`PF10433`	Beta-prop_RSE1_1st	105	447	5.4e-18	65.8
TkA05G416600	`PF23726`	Beta-prop_RSE1_2nd	380	412	1.6e-60	205.9
TkA05G416600	`PF23726`	Beta-prop_RSE1_2nd	563	995	1.6e-60	205.9
TkA05G416600	`PF03178`	CPSF_A	1072	1402	1.9e-87	294.3
TkA05G416600	`PF23726`	Beta-prop_RSE1_2nd	1133	1383	1.6e-60	205.9
TkA05G416600	`PF10433`	Beta-prop_RSE1_1st	1150	1241	5.4e-18	65.8

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9FGR0`	Arabidopsis thaliana	sp\|Q9FGR0\|CPSF1_ARATH Cleavage and polyadenylation specificity factor subunit 1	68.200%	Swiss-Prot	High
`Q7XWP1`	Oryza sativa subsp. japonica	sp\|Q7XWP1\|CPSF1_ORYSJ Probable cleavage and polyadenylation specificity factor subunit 1	64.500%	Swiss-Prot	High

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