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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_001983
Reference: OH-1004 Chr: Chr01 Coordinates: 38429589-38432861 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2250 bp · LXL04_001983|LXL04_001983|OH1004|cDNA

ATGCCACGTACTCCGATGGAAAACAAAAGCAGCTCTCAACCTCCTCCCATGGAGGTTACCGGTACTTCCCCTCTACCATACTTACTATACTTTCTAAATAAGCCAGATATTAAGATGATTTGTGTGGGTGACATGGATAATTCATCTGAGACTGGTCCAATTCCGGCCAGAATTCCCCGGCGTTCCGGCGACACTGATCATGATCTTGACAACAATAAGGATATTAGCTTGCGACAGTGGTTAGATAACCCAGAAAGAGC...

CDS

Download CDS FASTA

2250 bp · LXL04_001983|LXL04_001983|OH1004|CDS

ATGCCACGTACTCCGATGGAAAACAAAAGCAGCTCTCAACCTCCTCCCATGGAGGTTACCGGTACTTCCCCTCTACCATACTTACTATACTTTCTAAATAAGCCAGATATTAAGATGATTTGTGTGGGTGACATGGATAATTCATCTGAGACTGGTCCAATTCCGGCCAGAATTCCCCGGCGTTCCGGCGACACTGATCATGATCTTGACAACAATAAGGATATTAGCTTGCGACAGTGGTTAGATAACCCAGAAAGAGC...

Protein

Download Protein FASTA

749 aa · LXL04_001983|LXL04_001983|OH1004|PROTEIN

MPRTPMENKSSSQPPPMEVTGTSPLPYLLYFLNKPDIKMICVGDMDNSSETGPIPARIPRRSGDTDHDLDNNKDISLRQWLDNPERAIDPLENMHIFMQIVKIVTLAHSQGLVVHNIRPSCFVMSSFSHVSFIESASCSDSSSDSYQDVTSSQTDCYKHLPNDLLKRSENTWSEVTVKEEEEETKHVFPMKQILQMEMNWYTSPEETTGGPSSCASDVYRLGVLLFELYYPCSSPEEKNATMSTLKHRLFPPQFHCKWPK...

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.

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ID Mapping

Input IDLXL04_001983
Source versionOH-1004 / GCA_047496595.1_OSU_TarKok_2.0
Open Full ID Mapping
SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene IDLXL04_001983
LocationChr01:38429589-38432861 (-)
DescriptionSimilar to SPA3: Protein SPA1-RELATED 3
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g15354 Repressor of photomorphogenesis in the light.
The SPA1-like proteins SPA3 and SPA4 repress photomorphogenesis in the light.2003 · DOI: 10.1046/j.1365-313x.2003.01813.x
Functional and expression analysis of Arabidopsis SPA genes during seedling photomorphogenesis and adult growth.2006 · DOI: 10.1111/j.1365-313x.2006.02812.x
Arabidopsis SPA proteins regulate photoperiodic flowering and interact with the floral inducer CONSTANS to regulate its stability.2006 · DOI: 10.1242/dev.02481
At1g53090 Repressor of photomorphogenesis in the light.
The SPA1-like proteins SPA3 and SPA4 repress photomorphogenesis in the light.2003 · DOI: 10.1046/j.1365-313x.2003.01813.x
Functional and expression analysis of Arabidopsis SPA genes during seedling photomorphogenesis and adult growth.2006 · DOI: 10.1111/j.1365-313x.2006.02812.x
Arabidopsis SPA proteins regulate photoperiodic flowering and interact with the floral inducer CONSTANS to regulate its stability.2006 · DOI: 10.1242/dev.02481
At4g11110 Involved in suppression of photomorphogenesis in dark-grown seedlings.
The SPA quartet: a family of WD-repeat proteins with a central role in suppression of photomorphogenesis in arabidopsis.2004 · DOI: 10.1105/tpc.104.024216
Functional and expression analysis of Arabidopsis SPA genes during seedling photomorphogenesis and adult growth.2006 · DOI: 10.1111/j.1365-313x.2006.02812.x
UniProt: Q9SYX2 Controls normal photoperiodic flowering and regulates circadian rhythms. 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_001983 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009585 red, far-red light phototransduction Biological Process
GO:0009637 response to blue light Biological Process
GO:0009640 photomorphogenesis Biological Process
GO:0009658 chloroplast organization Biological Process
GO:0010017 red or far-red light signaling pathway Biological Process
GO:0010100 negative regulation of photomorphogenesis Biological Process
GO:0010114 response to red light Biological Process
GO:0010218 response to far red light Biological Process
GO:0016567 protein ubiquitination Biological Process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process
GO:0048575 short-day photoperiodism, flowering Biological Process
GO:2000028 regulation of photoperiodism, flowering Biological Process
KEGG gene cross-reference
ath:AT1G53090
ath:AT2G46340
ath:AT3G15354
ath:AT4G11110
These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.
Open Annotation Module

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.

Nucleus0.481
Rank 1 · LXL04_001983 · OH-1004
Cytoplasm0.434
Rank 2 · LXL04_001983 · OH-1004
Cell membrane0.076
Rank 3 · LXL04_001983 · OH-1004
Mitochondrion0.053
Rank 4 · LXL04_001983 · OH-1004
Lysosome / Vacuole0.051
Rank 5 · LXL04_001983 · 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.

PF25173.2Beta-prop_WDR3_1st438-602 aa
PF23389.2Beta-prop_WDR19_1st438-575 aa
PF25175.2Beta-prop_WDR5440-692 aa
PF25391.2WD40_Gbeta441-605 aa
PF24796.2WDR55445-645 aa
PF23775.2Beta-prop_RIG_2nd453-536 aa
PF25168.2Beta-prop_WDR36-Utp21_2nd454-595 aa
PF23383.2Beta-prop_IFT140_1st480-568 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_001983PF25173.2Beta-prop_WDR3_1st4386026e-2898.5
LXL04_001983PF23389.2Beta-prop_WDR19_1st4385758.2e-0935.6
LXL04_001983PF25175.2Beta-prop_WDR54406923.9e-34119.0
LXL04_001983PF25391.2WD40_Gbeta4416051e-1145.2
LXL04_001983PF24796.2WDR554456457.2e-1555.5
LXL04_001983PF23775.2Beta-prop_RIG_2nd4535368.1e-1039.3
LXL04_001983PF25168.2Beta-prop_WDR36-Utp21_2nd4545958.4e-1555.6
LXL04_001983PF23383.2Beta-prop_IFT140_1st4805681.6e-0834.4
LXL04_001983PF25174.2Beta-prop_THOC34906902.3e-2899.7
LXL04_001983PF29037.1DSE1_N4915637.9e-1348.9
LXL04_001983PF23409.2Beta-prop_EML4955628.8e-0936.0
LXL04_001983PF24105.2Beta-prop_CAF1B_HIR15025657.9e-1039.0
LXL04_001983PF24817.2WD40_WDHD1_1st5045703.7e-2279.6
LXL04_001983PF23414.2Beta-prop_EML_25046509.3e-1968.5
LXL04_001983PF25047.1Beta-prop_TEP1_2nd5046651.3e-1557.9
LXL04_001983PF23393.3Beta-prop_WDR90_POC16_2nd5045791.2e-0835.2

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q9LJR3Arabidopsis thalianaProtein SPA1-RELATED 356.010%Swiss-Protstrong database homology
Q94BM7Arabidopsis thalianaProtein SPA1-RELATED 458.355%Swiss-Protstrong database homology
Q9T014Arabidopsis thalianaProtein SPA1-RELATED 239.318%Swiss-Protmoderate database homology
Q9SYX2Arabidopsis thalianaProtein SUPPRESSOR OF PHYA-105 138.755%Swiss-Protmoderate database homology

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