LXL04_004470 | RubberDandelionOmics

Gene overview

LXL04_004470

Reference: OH-1004 Chr: Chr01 Coordinates: 137216730-137218283 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1353 bp · LXL04_004470|LXL04_004470|OH1004|cDNA

ATGTCTGGTGATGGGTTTTCATCAtctccttcttctctttctgCTTTCATACAAGACCCCATctcaaaccctaaccctaattcTTCAACATCAGCTAAACGAAAGCGCAACCTCCCCGGCACACCAGATCCAGATGCAGAAGTGATAGCTTTATCTCCGAAATCTCTGATGGCCACGAATCGGTTTTTATGCGAGATATGTAACAAAGGGTTTCAGAGAGACCAGAATTTGCAGCTTCATCGAAGAGGACACAATCTGCC...

CDS

Download CDS FASTA

1353 bp · LXL04_004470|LXL04_004470|OH1004|CDS

ATGTCTGGTGATGGGTTTTCATCATCTCCTTCTTCTCTTTCTGCTTTCATACAAGACCCCATCTCAAACCCTAACCCTAATTCTTCAACATCAGCTAAACGAAAGCGCAACCTCCCCGGCACACCAGATCCAGATGCAGAAGTGATAGCTTTATCTCCGAAATCTCTGATGGCCACGAATCGGTTTTTATGCGAGATATGTAACAAAGGGTTTCAGAGAGACCAGAATTTGCAGCTTCATCGAAGAGGACACAATCTGCC...

Protein

Download Protein FASTA

450 aa · LXL04_004470|LXL04_004470|OH1004|PROTEIN

MSGDGFSSSPSSLSAFIQDPISNPNPNSSTSAKRKRNLPGTPDPDAEVIALSPKSLMATNRFLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRNKLEVVKKKVYICPEKTCVHHDPSRALGDLTGVKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKICGTREYKCDCGTLFSRKDSFITHRAFCDALTEENSRMASFPMMSSTANLNFRNDLMMMNSGGGPGGGGVGLRFPGMYGGGMLESNTLDANGGKPRLPIWL...

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_004470`
TK1151 ID	TkA01G142830
OH-1004 ID	LXL04_004470
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
Protein coverage (%)	TK1151 99.778 / 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_004470

Location Chr01:137216730-137218283 (+)

Description Similar to JKD: Zinc finger protein JACKDAW

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g03150`	Transcription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action.	No verified direct reference in this release
`At3g45260`	Transcription factor that, together with JKD, regulates tissue boundaries and asymmetric cell division in roots by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action.	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
`At2g02080`	Transcription factor that may act a transcriptional activator of nuclear-encoded photosynthetic gene expression (Probable).	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_004470 · 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:0010075 regulation of meristem growth Biological Process

GO:0010336 gibberellic acid homeostasis Biological Process

GO:0010431 seed maturation Biological Process

GO:0034504 protein localization to nucleus Biological Process

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

KEGG gene cross-reference

ath:AT2G02080

ath:AT3G45260

ath:AT3G50700

ath:AT5G03150

ath:AT5G66730

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.

Nucleus0.983

Rank 1 · LXL04_004470 · OH-1004

Cytoplasm0.068

Rank 2 · LXL04_004470 · OH-1004

Cell membrane0.023

Rank 3 · LXL04_004470 · OH-1004

Endoplasmic reticulum0.014

Rank 4 · LXL04_004470 · OH-1004

Plastid0.009

Rank 5 · LXL04_004470 · 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-IDD100-134 aa

PF22995.3C2CH-3rd_BIRD-IDD138-162 aa

PF22992.3C2CH-4th_BIRD-IDD165-204 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004470	`PF22996.3`	C2H2-2nd_BIRD-IDD	100	134	1.4e-21	76.9
LXL04_004470	`PF22995.3`	C2CH-3rd_BIRD-IDD	138	162	9.4e-15	54.7
LXL04_004470	`PF22992.3`	C2CH-4th_BIRD-IDD	165	204	3.7e-24	85.0

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q700D2`	Arabidopsis thaliana	Zinc finger protein JACKDAW	81.188%	Swiss-Prot	weak database homology
`Q944L3`	Arabidopsis thaliana	Zinc finger protein BALDIBIS	87.059%	Swiss-Prot	weak database homology
`Q9SCQ6`	Arabidopsis thaliana	Zinc finger protein GAI-ASSOCIATED FACTOR 1	83.908%	Swiss-Prot	weak database homology
`Q8GYC1`	Arabidopsis thaliana	Protein indeterminate-domain 4, chloroplastic	43.590%	Swiss-Prot	moderate database homology
`Q9LVQ7`	Arabidopsis thaliana	Zinc finger protein ENHYDROUS	82.759%	Swiss-Prot	weak database homology

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