LXL04_015717 | RubberDandelionOmics

Gene overview

LXL04_015717

Reference: OH-1004 Chr: Chr03 Coordinates: 81750512-81755199 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1863 bp · LXL04_015717|LXL04_015717|OH1004|cDNA

ATGGCCGCAGCTTCTTCATCAACTTCATTTTATGGAGCAAAATCAGACGAAGAACAACATGTTTCTTCAATACCTACTTCTTCTTCAACTATTCAATCAGCTTCGGCCcaacagaagaagaagagaagcCTTCCAGGAACTCCAAGCAAGTACCCAAACACTTATCTTATTTTCTTCATTTCGCTTCTTGAAATCTATAACTTTCATCCAGATGCTGAGGTGATAGCGTTGTCACCAAAGACTCTAATGGCAACAAACCG...

CDS

Download CDS FASTA

1863 bp · LXL04_015717|LXL04_015717|OH1004|CDS

ATGGCCGCAGCTTCTTCATCAACTTCATTTTATGGAGCAAAATCAGACGAAGAACAACATGTTTCTTCAATACCTACTTCTTCTTCAACTATTCAATCAGCTTCGGCCCAACAGAAGAAGAAGAGAAGCCTTCCAGGAACTCCAAGCAAGTACCCAAACACTTATCTTATTTTCTTCATTTCGCTTCTTGAAATCTATAACTTTCATCCAGATGCTGAGGTGATAGCGTTGTCACCAAAGACTCTAATGGCAACAAACCG...

Protein

Download Protein FASTA

620 aa · LXL04_015717|LXL04_015717|OH1004|PROTEIN

MAAASSSTSFYGAKSDEEQHVSSIPTSSSTIQSASAQQKKKRSLPGTPSKYPNTYLIFFISLLEIYNFHPDAEVIALSPKTLMATNRFICEVCNKGFQREQNLQLHRRGHNLPWKLKQKSNKEVKRKVYLCPEPSCVHHDPSRALGDLTGIKKHYSRKHGEKKYKCEKCSKKYAVQSDWKAHSKTCGTREYRCDCGTLFSRRDSFITHRAFCDALAQETARHPSTLGTIGSHLFGNHLGNSMNLGLSQVGSQISQLHDHP...

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_015717`
TK1151 ID	TkA02G295010
OH-1004 ID	LXL04_015717
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	71.800
Protein coverage (%)	TK1151 97.284 / OH-1004 82.903 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

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 ID LXL04_015717

Location Chr03:81750512-81755199 (+)

Description Similar to IDD4: Protein indeterminate-domain 4, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g02080`	Transcription factor that may act a transcriptional activator of nuclear-encoded photosynthetic gene expression (Probable).	No verified direct reference in this release
`At2g02070`	Transcription factor acting as a positive regulator of the starch synthase SS4.	Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model.2012 · DOI: 10.1186/1752-0509-6-100
`At1g14580`	Probable transcription factor.	No verified direct reference in this release
`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_015717 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002221 pattern recognition receptor signaling pathway Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0008356 asymmetric cell division Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

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

GO:0010029 regulation of seed germination Biological Process

GO:0010336 gibberellic acid homeostasis Biological Process

GO:0010431 seed maturation Biological Process

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

GO:0048364 root development Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G14580

ath:AT2G02070

ath:AT2G02080

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.

Nucleus0.961

Rank 1 · LXL04_015717 · OH-1004

Cytoplasm0.152

Rank 2 · LXL04_015717 · OH-1004

Cell membrane0.016

Rank 3 · LXL04_015717 · OH-1004

Mitochondrion0.013

Rank 4 · LXL04_015717 · OH-1004

Endoplasmic reticulum0.007

Rank 5 · LXL04_015717 · 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.

PF22996.3C2H2-2nd_BIRD-IDD125-159 aa

PF22995.3C2CH-3rd_BIRD-IDD163-187 aa

PF22992.3C2CH-4th_BIRD-IDD190-225 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015717	`PF22996.3`	C2H2-2nd_BIRD-IDD	125	159	2.4e-22	79.4
LXL04_015717	`PF22995.3`	C2CH-3rd_BIRD-IDD	163	187	6.4e-14	52.0
LXL04_015717	`PF22992.3`	C2CH-4th_BIRD-IDD	190	225	3.2e-24	85.2

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

Protein	Organism	Description	Identity	Database	Confidence
`Q8GYC1`	Arabidopsis thaliana	Protein indeterminate-domain 4, chloroplastic	45.772%	Swiss-Prot	moderate database homology
`Q9ZUL3`	Arabidopsis thaliana	Protein indeterminate-domain 5, chloroplastic	41.721%	Swiss-Prot	moderate database homology
`Q8RWX7`	Arabidopsis thaliana	Protein indeterminate-domain 6, chloroplastic	66.102%	Swiss-Prot	weak database homology
`Q9SCQ6`	Arabidopsis thaliana	Zinc finger protein GAI-ASSOCIATED FACTOR 1	77.049%	Swiss-Prot	weak database homology
`Q9LVQ7`	Arabidopsis thaliana	Zinc finger protein ENHYDROUS	75.956%	Swiss-Prot	weak database homology

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