LXL04_011118 | RubberDandelionOmics

Gene overview

LXL04_011118

Reference: OH-1004 Chr: Chr02 Coordinates: 158211973-158213982 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1170 bp · LXL04_011118|LXL04_011118|OH1004|cDNA

ATGTTAGACAACagcgaccaccaccacctccaccaccatcTCACTGCTGCGCCTGCACCTGgtccatcttcttcttctgatcCTTTTCTTTCCCCAGATAATGGTCTTTCCAACAAACGAAAAAGGCGTCCTGCTGGTACTCCAGATCCGGATGCGGAGGTGGTATCTTTATCGCCGAAGACATTGTTGGAGTCGGATAGATACGTATGTGAGATCTGTAATCAAGGGTTTCAACGGGATCAGAATTTGCAGATGCACCG...

CDS

Download CDS FASTA

1170 bp · LXL04_011118|LXL04_011118|OH1004|CDS

ATGTTAGACAACAGCGACCACCACCACCTCCACCACCATCTCACTGCTGCGCCTGCACCTGGTCCATCTTCTTCTTCTGATCCTTTTCTTTCCCCAGATAATGGTCTTTCCAACAAACGAAAAAGGCGTCCTGCTGGTACTCCAGATCCGGATGCGGAGGTGGTATCTTTATCGCCGAAGACATTGTTGGAGTCGGATAGATACGTATGTGAGATCTGTAATCAAGGGTTTCAACGGGATCAGAATTTGCAGATGCACCG...

Protein

Download Protein FASTA

389 aa · LXL04_011118|LXL04_011118|OH1004|PROTEIN

MLDNSDHHHLHHHLTAAPAPGPSSSSDPFLSPDNGLSNKRKRRPAGTPDPDAEVVSLSPKTLLESDRYVCEICNQGFQRDQNLQMHRRRHKVPWKLLKRETPEVKKKVFVCPEPSCLHHDPCHALGDLVGIKKHFRRKHSNDKQWVCDKCSKGYAVQSDYKAHLKTCGTRGHSCDCGRVFSRVESFIEHQDACTVRRVHPDLPAFQQACSSRTASSTSPSSDTNPSLQRLQQIPPSESTFFPDPRNKLELQLLPSSSLYE...

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_011118`
TK1151 ID	TkA03G566480
OH-1004 ID	LXL04_011118
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	100.000
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_011118

Location Chr02:158211973-158213982 (+)

Description Similar to IDD14: Protein indeterminate-domain 14

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g68130`	Transcription factor regulating starch metabolism by binding directly to the promoter of QQS.	Two splice variants of the IDD14 transcription factor competitively form nonfunctional heterodimers which may regulate starch metabolism.2011 · DOI: 10.1038/ncomms1303 The arabidopsis IDD14, IDD15, and IDD16 cooperatively regulate lateral organ morphogenesis and gravitropism by promoting auxin biosynthesis and transport.2013 · DOI: 10.1371/journal.pgen.1003759
`At2g01940`	Transcription factor involved in inflorescence stems gravitropism, probably by regulating starch accumulation in amyloplasts of graviperceptive cells.	A C2H2-type zinc finger protein, SGR5, is involved in early events of gravitropism in Arabidopsis inflorescence stems.2006 · DOI: 10.1111/j.1365-313x.2006.02807.x Altered gravitropic response, amyloplast sedimentation and circumnutation in the Arabidopsis shoot gravitropism 5 mutant are associated with reduced starch levels.2008 · DOI: 10.1007/s11103-008-9301-0 The arabidopsis IDD14, IDD15, and IDD16 cooperatively regulate lateral organ morphogenesis and gravitropism by promoting auxin biosynthesis and transport.2013 · DOI: 10.1371/journal.pgen.1003759 Mutations in the SGR4, SGR5 and SGR6 loci of Arabidopsis thaliana alter the shoot gravitropism.1997 · DOI: 10.1093/oxfordjournals.pcp.a029201
`At1g25250`	Transcription factor regulating lateral organ morphogenesis and gravitropic responses.	The arabidopsis IDD14, IDD15, and IDD16 cooperatively regulate lateral organ morphogenesis and gravitropism by promoting auxin biosynthesis and transport.2013 · DOI: 10.1371/journal.pgen.1003759
`At3g50700`	Transcription factor that acts as a positive regulator of gibberellin (GA) action, homeostasis and signaling.	No verified direct reference in this release
`At5g66730`	Transcription factor promoting the transition to germination by regulating light and hormonal signaling during seed maturation.	The Arabidopsis C2H2 zinc finger INDETERMINATE DOMAIN1/ENHYDROUS promotes the transition to germination by regulating light and hormonal signaling during seed maturation.2011 · DOI: 10.1105/tpc.111.085134 DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis.2014 · DOI: 10.1105/tpc.114.125690

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011118 · 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:0009590 detection of gravity Biological Process

GO:0009630 gravitropism Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009937 regulation of gibberellic acid mediated signaling pathway Biological Process

GO:0009959 negative gravitropism Biological Process

GO:0009965 leaf morphogenesis Biological Process

GO:0010029 regulation of seed germination Biological Process

GO:0010031 circumnutation Biological Process

GO:0010336 gibberellic acid homeostasis Biological Process

GO:0010431 seed maturation Biological Process

KEGG gene cross-reference

ath:AT1G25250

ath:AT1G68130

ath:AT2G01940

ath:AT3G50700

ath:AT5G66730

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.

Nucleus0.975

Rank 1 · LXL04_011118 · OH-1004

Cytoplasm0.082

Rank 2 · LXL04_011118 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_011118 · OH-1004

Endoplasmic reticulum0.012

Rank 4 · LXL04_011118 · OH-1004

Plastid0.009

Rank 5 · LXL04_011118 · 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.

PF22996.3C2H2-2nd_BIRD-IDD105-139 aa

PF22995.3C2CH-3rd_BIRD-IDD144-168 aa

PF22992.3C2CH-4th_BIRD-IDD172-194 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011118	`PF22996.3`	C2H2-2nd_BIRD-IDD	105	139	1.6e-18	67.1
LXL04_011118	`PF22995.3`	C2CH-3rd_BIRD-IDD	144	168	3.8e-14	52.8
LXL04_011118	`PF22992.3`	C2CH-4th_BIRD-IDD	172	194	2.5e-06	27.9

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
`Q9C9X7`	Arabidopsis thaliana	Protein indeterminate-domain 14	59.269%	Swiss-Prot	strong database homology
`F4IPE3`	Arabidopsis thaliana	Zinc finger protein SHOOT GRAVITROPISM 5	56.635%	Swiss-Prot	strong database homology
`Q9FRH4`	Arabidopsis thaliana	Protein indeterminate-domain 16	57.465%	Swiss-Prot	strong database homology
`Q9SCQ6`	Arabidopsis thaliana	Zinc finger protein GAI-ASSOCIATED FACTOR 1	65.605%	Swiss-Prot	weak database homology
`Q9LVQ7`	Arabidopsis thaliana	Zinc finger protein ENHYDROUS	65.385%	Swiss-Prot	weak database homology

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