LXL04_004840 | RubberDandelionOmics

Gene overview

LXL04_004840

Reference: OH-1004 Chr: Chr01 Coordinates: 148526705-148528353 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

951 bp · LXL04_004840|LXL04_004840|OH1004|cDNA

ATGAATTCTGTGTATTACAAGCAACATGATGATGGAATCGCTTCAAACCCAGTGGGTTCACTGTCATCGGCTTCGGGTCCATGGTGGAGTGGACTTGTGACTCATTCCACTTTTGAAGGTCAAATGAAGCCTTCATCAATGGAAAATTGTGGAGAACAACTCATGCCGATTGCCCCTAAACCATCTTCGCATAGCACAGATCAAGGGAATACCGCTCATTCTAATACCTTTCCTGGTGACTGCAAGAATTCATCAAAAGG...

CDS

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951 bp · LXL04_004840|LXL04_004840|OH1004|CDS

ATGAATTCTGTGTATTACAAGCAACATGATGATGGAATCGCTTCAAACCCAGTGGGTTCACTGTCATCGGCTTCGGGTCCATGGTGGAGTGGACTTGTGACTCATTCCACTTTTGAAGGTCAAATGAAGCCTTCATCAATGGAAAATTGTGGAGAACAACTCATGCCGATTGCCCCTAAACCATCTTCGCATAGCACAGATCAAGGGAATACCGCTCATTCTAATACCTTTCCTGGTGACTGCAAGAATTCATCAAAAGG...

Protein

Download Protein FASTA

316 aa · LXL04_004840|LXL04_004840|OH1004|PROTEIN

MNSVYYKQHDDGIASNPVGSLSSASGPWWSGLVTHSTFEGQMKPSSMENCGEQLMPIAPKPSSHSTDQGNTAHSNTFPGDCKNSSKGQKPVQFESAFSMQSAPQEYGGQLELGFGQQAVICGKYTYGDQYYGMIPGCGPQITGRIMLPLNMSTDDGPIFVNAKQYHGIIRRRRSRAKAEMAKKVSKGRKPYLHLSRHLHAKRRPRGCGGRFLNTKELEKVKAVNLQSKITEHPIGSQRSEVLQSDHEMNANRSHISGSEV...

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_004840`
TK1151 ID	TkA01G102420
OH-1004 ID	LXL04_004840
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.400
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_004840

Location Chr01:148526705-148528353 (+)

Description Similar to NFYA10: Nuclear transcription factor Y subunit A-10

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g06510`	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.	No verified direct reference in this release
`At3g05690`	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters (By similarity).	No verified direct reference in this release
`At1g72830`	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.	No verified direct reference in this release
`At1g30500`	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.	No verified direct reference in this release
`At2g34720`	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004840 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0009408 response to heat Biological Process

GO:0009567 double fertilization forming a zygote and endosperm Biological Process

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

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0048510 regulation of timing of transition from vegetative to reproductive phase Biological Process

GO:0005634 nucleus Cellular Component

GO:0016602 CCAAT-binding factor complex Cellular Component

GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific Molecular Function

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G30500

ath:AT1G72830

ath:AT2G34720

ath:AT3G05690

ath:AT5G06510

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.

Nucleus0.960

Rank 1 · LXL04_004840 · OH-1004

Cytoplasm0.115

Rank 2 · LXL04_004840 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_004840 · OH-1004

Endoplasmic reticulum0.013

Rank 4 · LXL04_004840 · OH-1004

Mitochondrion0.010

Rank 5 · LXL04_004840 · 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.

PF02045.22CBFB_NFYA127-221 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004840	`PF02045.22`	CBFB_NFYA	127	221	3.7e-34	118.3

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
`Q8LFU0`	Arabidopsis thaliana	Nuclear transcription factor Y subunit A-10	39.610%	Swiss-Prot	moderate database homology
`Q9M9X4`	Arabidopsis thaliana	Nuclear transcription factor Y subunit A-2	43.346%	Swiss-Prot	moderate database homology
`Q93ZH2`	Arabidopsis thaliana	Nuclear transcription factor Y subunit A-3	35.841%	Swiss-Prot	moderate database homology
`Q84JP1`	Arabidopsis thaliana	Nuclear transcription factor Y subunit A-7	55.556%	Swiss-Prot	weak database homology
`Q8VY64`	Arabidopsis thaliana	Nuclear transcription factor Y subunit A-4	50.000%	Swiss-Prot	weak database homology

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