LXL04_012502 | RubberDandelionOmics

Gene overview

LXL04_012502

Reference: OH-1004 Chr: Chr03 Coordinates: 13360571-13361695 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

498 bp · LXL04_012502|LXL04_012502|OH1004|cDNA

ATGGCGGATTGTCCTGGGAGTCCGGCCGGTGGGAGCCACGAAAGCGGCGGTGAACAGAGTCCTCAGTCGAACTCGAACATCAGGGAGCAGGATAGGTTTCTCCCGATCGCTAACATAAGCCGGATCATGAAAAAGGCATTGCCTGCTAACGGGAAGATCGCGAAAGACGCTAAAGACACCGTTCAGGAATGCGTTTCTGAGTTCATCAGTTTCGTTACTAGCGAGGCCAGTGATAAGTGTCAGAAAGAGAAGAGGAAGAC...

CDS

Download CDS FASTA

498 bp · LXL04_012502|LXL04_012502|OH1004|CDS

ATGGCGGATTGTCCTGGGAGTCCGGCCGGTGGGAGCCACGAAAGCGGCGGTGAACAGAGTCCTCAGTCGAACTCGAACATCAGGGAGCAGGATAGGTTTCTCCCGATCGCTAACATAAGCCGGATCATGAAAAAGGCATTGCCTGCTAACGGGAAGATCGCGAAAGACGCTAAAGACACCGTTCAGGAATGCGTTTCTGAGTTCATCAGTTTCGTTACTAGCGAGGCCAGTGATAAGTGTCAGAAAGAGAAGAGGAAGAC...

Protein

Download Protein FASTA

165 aa · LXL04_012502|LXL04_012502|OH1004|PROTEIN

MADCPGSPAGGSHESGGEQSPQSNSNIREQDRFLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFVTSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLCRYREGDAKGSASARGDGSGKKDPVGPQLVPNSQYPHQGSFTQGMNFLNSHV

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_012502`
TK1151 ID	TkA02G557440
OH-1004 ID	LXL04_012502
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	98.800
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

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Basic Information and Functional Annotation

Gene ID LXL04_012502

Location Chr03:13360571-13361695 (+)

Description Similar to NFYB8: Nuclear transcription factor Y subunit B-8

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g37060`	Component of the NF-Y/HAP transcription factor complex.	No verified direct reference in this release
`At3g53340`	Component of the NF-Y/HAP transcription factor complex.	No verified direct reference in this release
`At2g38880`	Component of the NF-Y/HAP transcription factor complex (By similarity).	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0834400`	Component of the NF-Y/HAP transcription factor complex.	OsHAP3 genes regulate chloroplast biogenesis in rice.2003 · DOI: 10.1046/j.1365-313x.2003.01897.x

Functional annotation source

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Functional annotation source: OH1004 · LXL04_012502 · 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:0009414 response to water deprivation Biological Process

GO:0019760 glucosinolate metabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0016602 CCAAT-binding factor complex Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

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

GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

ath:AT2G37060

ath:AT2G38880

ath:AT3G53340

dosa:Os01g0834400

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.

Nucleus0.949

Rank 1 · LXL04_012502 · OH-1004

Cytoplasm0.186

Rank 2 · LXL04_012502 · OH-1004

Cell membrane0.020

Rank 3 · LXL04_012502 · OH-1004

Mitochondrion0.018

Rank 4 · LXL04_012502 · OH-1004

Endoplasmic reticulum0.011

Rank 5 · LXL04_012502 · OH-1004

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.

PF00125.31Histone25-97 aa

PF00808.30CBFD_NFYB_HMF33-97 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012502	`PF00125.31`	Histone	25	97	1e-05	26.5
LXL04_012502	`PF00808.30`	CBFD_NFYB_HMF	33	97	2.3e-28	99.0

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
`Q8VYK4`	Arabidopsis thaliana	Nuclear transcription factor Y subunit B-8	74.834%	Swiss-Prot	strong database homology
`Q67XJ2`	Arabidopsis thaliana	Nuclear transcription factor Y subunit B-10	75.352%	Swiss-Prot	strong database homology
`Q9SLG0`	Arabidopsis thaliana	Nuclear transcription factor Y subunit B-1	75.735%	Swiss-Prot	strong database homology
`Q5QMG3`	Oryza sativa subsp. japonica	Nuclear transcription factor Y subunit B-2	66.875%	Swiss-Prot	strong database homology

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