LXL04_021563 | RubberDandelionOmics

Gene overview

LXL04_021563

Reference: OH-1004 Chr: Chr04 Coordinates: 132412507-132413972 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

648 bp · LXL04_021563|LXL04_021563|OH1004|cDNA

ATGCAGCAGCAACAGCATCAACAACCACCGCAATCGCAACTGCAACCGCCCACCTTAAACTCCGGTGCTCCTTTTTCTTCCAATGCGATCACCTCCGACCAGATTCAAAAGTGTCTGGATGACAACAAAAACTTGATTATGGCAATATTGGAAAATCAAAATCTTGGGAAATTTCAGGAGTGTGCTCAGTATCAAGCCATTCTCCAAAAGAACTTAATGTATTTAGCTGCAATTGCTGATGCTCAACCACCAACACAACA...

CDS

Download CDS FASTA

648 bp · LXL04_021563|LXL04_021563|OH1004|CDS

ATGCAGCAGCAACAGCATCAACAACCACCGCAATCGCAACTGCAACCGCCCACCTTAAACTCCGGTGCTCCTTTTTCTTCCAATGCGATCACCTCCGACCAGATTCAAAAGTGTCTGGATGACAACAAAAACTTGATTATGGCAATATTGGAAAATCAAAATCTTGGGAAATTTCAGGAGTGTGCTCAGTATCAAGCCATTCTCCAAAAGAACTTAATGTATTTAGCTGCAATTGCTGATGCTCAACCACCAACACAACA...

Protein

Download Protein FASTA

215 aa · LXL04_021563|LXL04_021563|OH1004|PROTEIN

MQQQQHQQPPQSQLQPPTLNSGAPFSSNAITSDQIQKCLDDNKNLIMAILENQNLGKFQECAQYQAILQKNLMYLAAIADAQPPTQQPSTPQMPPNSIPQQPNNYMQQQHQITATQQGGIGGGGGGVPKLPFQLNALRTQDQQQQLLQFQQQQQQQQLQAQMGMRPSAQNGMLGMHQAMQSALAGNPGSLMDGRGNKQDGSETAASGGGGGNRES

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_021563`
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_021563

Location Chr04:132412507-132413972 (+)

Description Similar to GIF3: GRF1-interacting factor 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g00850`	Transcription coactivator that plays a role in the regulation of cell expansion in leaf and cotyledons tissues (By similarity).	The Arabidopsis GRF-INTERACTING FACTOR gene family performs an overlapping function in determining organ size as well as multiple developmental properties.2009 · DOI: 10.1104/pp.109.141838
`At1g01160`	Transcription coactivator that plays a role in the regulation of cell expansion in leaf and cotyledons tissues (By similarity).	The Arabidopsis GRF-INTERACTING FACTOR gene family performs an overlapping function in determining organ size as well as multiple developmental properties.2009 · DOI: 10.1104/pp.109.141838
`At5g28640`	Transcription coactivator that plays a role in the regulation of cell expansion in leaf and cotyledons tissues.	A transcriptional coactivator, AtGIF1, is involved in regulating leaf growth and morphology in Arabidopsis.2004 · DOI: 10.1073/pnas.0405450101 The transcription factor AtGRF5 and the transcription coactivator AN3 regulate cell proliferation in leaf primordia of Arabidopsis thaliana.2005 · DOI: 10.1111/j.1365-313x.2005.02429.x The Arabidopsis GRF-INTERACTING FACTOR gene family performs an overlapping function in determining organ size as well as multiple developmental properties.2009 · DOI: 10.1104/pp.109.141838 Stable establishment of cotyledon identity during embryogenesis in Arabidopsis by ANGUSTIFOLIA3 and HANABA TARANU.2012 · DOI: 10.1242/dev.081547

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0733600`	Transcription coactivator that plays a role in the regulation of meristematic function in leaves, stems and inflorescences.	The OsmiR396c-OsGRF4-OsGIF1 regulatory module determines grain size and yield in rice.2016 · DOI: 10.1111/pbi.12569 OsGIF1 Positively Regulates the Sizes of Stems, Leaves, and Grains in Rice.2017 · DOI: 10.3389/fpls.2017.01730 Conserved functional control, but distinct regulation, of cell proliferation in rice and Arabidopsis leaves revealed by comparative analysis of GRF-INTERACTING FACTOR 1 orthologs.2018 · DOI: 10.1242/dev.159624

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021563 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0008283 cell population proliferation Biological Process

GO:0009955 adaxial/abaxial pattern specification Biological Process

GO:0010449 root meristem growth Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0010582 floral meristem determinacy Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0045787 positive regulation of cell cycle Biological Process

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

GO:0048316 seed development Biological Process

GO:0048366 leaf development Biological Process

GO:0048825 cotyledon development Biological Process

KEGG gene cross-reference

ath:AT1G01160

ath:AT4G00850

ath:AT5G28640

dosa:Os03g0733600

zma:100101544

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_021563 · OH-1004

Cytoplasm0.205

Rank 2 · LXL04_021563 · OH-1004

Mitochondrion0.015

Rank 3 · LXL04_021563 · OH-1004

Cell membrane0.013

Rank 4 · LXL04_021563 · OH-1004

Endoplasmic reticulum0.008

Rank 5 · LXL04_021563 · 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.

PF05030.18SSXT29-87 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021563	`PF05030.18`	SSXT	29	87	6.3e-22	77.7

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q93VH6`	Arabidopsis thaliana	GRF1-interacting factor 3	46.977%	Swiss-Prot	moderate database homology
`Q9MAL9`	Arabidopsis thaliana	GRF1-interacting factor 2	44.865%	Swiss-Prot	moderate database homology
`Q8L8A5`	Arabidopsis thaliana	GRF1-interacting factor 1	66.667%	Swiss-Prot	weak database homology
`Q6AVI1`	Oryza sativa subsp. japonica	GRF-interacting factor 1	55.682%	Swiss-Prot	weak database homology

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