TkAUNG024010 | RubberDandelionOmics

Gene overview

TkAUNG024010

Reference: TK1151 Chr: ChrUn Coordinates: 6442254-6445197 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2152 bp · TkAUNG024010|TK1151|cDNA

AGATCTTGAAATATGTTTAATTAATATAGAAAATCACGCTCTAACTTGATTTTCTTTCGTCACAATCTCTCTCCATTCTAGGGCCAATACAGAAGAAAACAATGGCGATCGAATGTCTAGTTCTAGGCGCAGGACAAGAGGTAGGGAAGAGCTGCGTTATAGTATCTATTCACGGAAAAAGGATCATGTTCGATTGTGGGATGCACATGGGTTACTCCGATCACCGCCGTTACCCTGATTTCTCTCTCATTTCACAATCC...

CDS

Download CDS FASTA

1860 bp · TkAUNG024010|TK1151|CDS

ATGGCGATCGAATGTCTAGTTCTAGGCGCAGGACAAGAGGTAGGGAAGAGCTGCGTTATAGTATCTATTCACGGAAAAAGGATCATGTTCGATTGTGGGATGCACATGGGTTACTCCGATCACCGCCGTTACCCTGATTTCTCTCTCATTTCACAATCCGGCGACTTCAATGCCGCCCTTTCATGCATCATTATCACTCACTTTCACTTGGATCATATCGGTGCTCTTCCGTACTTCACTGAAGTTTGTGGTTACACCGG...

Protein

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619 aa · TkAUNG024010|TK1151|PROTEIN

MAIECLVLGAGQEVGKSCVIVSIHGKRIMFDCGMHMGYSDHRRYPDFSLISQSGDFNAALSCIIITHFHLDHIGALPYFTEVCGYTGPIYMTYPTKALAPLMLEDYRKVMVGRGEEQQFTHENILDCMKKVTAVGLKQNVQVDKDLQIRAYYAGHVLGAAMFYACVEDSGIVYTGDYNMTPDRHLGAAQIDRLQLDLLITESTYATTIRDSKYAREREFLKAVHKCVANGGKVLIPTFALGRAQELCILLDDYWERMNLK...

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	`TkAUNG024010`
TK1151 ID	TkAUNG024010
OH-1004 ID	LXL04_025103
Relationship / confidence	Multi Candidate From Tk1151 / Complex relationship
Protein identity (%)	99.300
Protein coverage (%)	TK1151 97.738 / OH-1004 95.728 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 TkAUNG024010

Location ChrUn:6442254-6445197 (-)

Description No functional description available

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g01730`	Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play 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.	Unique features of plant cleavage and polyadenylation specificity factor revealed by proteomic studies.2009 · DOI: 10.1104/pp.109.142729

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_025103 · 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:0006366 transcription by RNA polymerase II Biological Process

GO:0006368 transcription elongation by RNA polymerase II Biological Process

GO:0006397 mRNA processing Biological Process

GO:0010197 polar nucleus fusion Biological Process

GO:0016180 snRNA processing Biological Process

GO:0034243 regulation of transcription elongation by RNA polymerase II Biological Process

GO:0034472 snRNA 3'-end processing Biological Process

GO:0160240 RNA polymerase II transcription initiation surveillance Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT2G01730

ddi:DDB_G0278189

gga:419418

mmu:71957

rno:298688

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.

Nucleus0.720

Rank 1 · TkAUNG024010 · TK1151

Cytoplasm0.350

Rank 2 · TkAUNG024010 · TK1151

Mitochondrion0.055

Rank 3 · TkAUNG024010 · TK1151

Cell membrane0.029

Rank 4 · TkAUNG024010 · TK1151

Endoplasmic reticulum0.023

Rank 5 · TkAUNG024010 · 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.

PF00753Lactamase_B16-182 aa

PF23023Anti-Pycsar_Apyc117-183 aa

PF16661Lactamase_B_621-190 aa

PF12706Lactamase_B_227-203 aa

PF26524ARM_7108-159 aa

PF10996Beta-Casp243-361 aa

PF07521RMMBL377-435 aa

PF12706Lactamase_B_2391-413 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkAUNG024010	`PF00753`	Lactamase_B	16	182	3.7e-12	47.3
TkAUNG024010	`PF23023`	Anti-Pycsar_Apyc1	17	183	9.3e-09	36.1
TkAUNG024010	`PF16661`	Lactamase_B_6	21	190	7.9e-19	68.5
TkAUNG024010	`PF12706`	Lactamase_B_2	27	203	9.1e-05	22.8
TkAUNG024010	`PF26524`	ARM_7	108	159	0.1	12.6
TkAUNG024010	`PF10996`	Beta-Casp	243	361	6.1e-27	95.3
TkAUNG024010	`PF07521`	RMMBL	377	435	5.2e-17	62.3
TkAUNG024010	`PF12706`	Lactamase_B_2	391	413	9.1e-05	22.8

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
`Q8GUU3`	Arabidopsis thaliana	sp\|Q8GUU3\|CPS3B_ARATH Cleavage and polyadenylation specificity factor subunit 3-II	65.300%	Swiss-Prot	High

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