LXL04_021704 | RubberDandelionOmics

Gene overview

LXL04_021704

Reference: OH-1004 Chr: Chr04 Coordinates: 135604944-135616340 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4413 bp · LXL04_021704|LXL04_021704|OH1004|cDNA

ATGGTGATTGATAAGGCTACATATTCAAGTCCATCTCACTACTTTGTGTATACACAATGGCAATCACATACTGCTGAATCCTCCCTCTCTCTTGCTCTCCCAAAGCAATCCTACATTTCACGAATCATCGTTGAGAAATCTAATTACAAAGACGAAATGAGCTACGCGGCATACAAATTGATGCACCCGCCCACCGGAATCGACAACTGCGCATCAGGATTCATCACGCATTCTCCCGCCGACTTCGCTTCCCGCATTCT...

CDS

Download CDS FASTA

4413 bp · LXL04_021704|LXL04_021704|OH1004|CDS

ATGGTGATTGATAAGGCTACATATTCAAGTCCATCTCACTACTTTGTGTATACACAATGGCAATCACATACTGCTGAATCCTCCCTCTCTCTTGCTCTCCCAAAGCAATCCTACATTTCACGAATCATCGTTGAGAAATCTAATTACAAAGACGAAATGAGCTACGCGGCATACAAATTGATGCACCCGCCCACCGGAATCGACAACTGCGCATCAGGATTCATCACGCATTCTCCCGCCGACTTCGCTTCCCGCATTCT...

Protein

Download Protein FASTA

1470 aa · LXL04_021704|LXL04_021704|OH1004|PROTEIN

MVIDKATYSSPSHYFVYTQWQSHTAESSLSLALPKQSYISRIIVEKSNYKDEMSYAAYKLMHPPTGIDNCASGFITHSPADFASRILPAPTDEIDPVWPSAPTPGVGPIPNLIVTAANVLEVYTVRVQEDGNSTSKDSSTVAQPQRGGVMAGLSGASLELVCSYRLHGNVESVGVLSSGAEERTSGRRRDSIILTFEDAKISILEFDDSVYGLRTSSMHCFEGPQWLHLKKGRESFARGPFIKADPLGRCAGVLVYGLQM...

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	`LXL04_021704`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_021704

Location Chr04:135604944-135616340 (-)

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

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Functional annotation source: OH1004 · LXL04_021704 · GCA_047496595.1_OSU_TarKok_2.0.

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.

Nucleus0.768

Rank 1 · LXL04_021704 · OH-1004

Cytoplasm0.252

Rank 2 · LXL04_021704 · OH-1004

Lysosome / Vacuole0.049

Rank 3 · LXL04_021704 · OH-1004

Golgi apparatus0.046

Rank 4 · LXL04_021704 · OH-1004

Cell membrane0.031

Rank 5 · LXL04_021704 · OH-1004

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.

PF10433.16Beta-prop_RSE1_1st157-499 aa

PF23726.2Beta-prop_RSE1_2nd615-1040 aa

PF03178.22CPSF_A1104-1434 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021704	`PF10433.16`	Beta-prop_RSE1_1st	157	499	5.7e-18	65.8
LXL04_021704	`PF23726.2`	Beta-prop_RSE1_2nd	615	1040	4.6e-55	187.9
LXL04_021704	`PF03178.22`	CPSF_A	1104	1434	2.9e-87	293.7

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
`Q9FGR0`	Arabidopsis thaliana	Cleavage and polyadenylation specificity factor subunit 1	66.964%	Swiss-Prot	strong database homology
`Q7XWP1`	Oryza sativa subsp. japonica	Probable cleavage and polyadenylation specificity factor subunit 1	63.172%	Swiss-Prot	strong database homology

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