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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_039364
Reference: OH-1004 Chr: JAJTUU010000010.1 Coordinates: 4399193-4405573 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1521 bp · LXL04_039364|LXL04_039364|OH1004|cDNA

ATGGCGAATCAGCTGTACGGTTCCAGCTCCTACGGGTATGGGGGAGGATCCAATTCGTCAAGCATATACACTTCTAAATCCATCGGTGAGCAGTACGTCCCCTCGGACCCATCGCACCTCACTTCGTCTAGGTATTTAGGCTCAGATCCCCTGTCAGCGTCTTCCAATTTGTTCAGCTTTTCATCAATCAGCGACAGAGCTCCATCCATGCTGTACAACCAGGATACTATCGGCAGTGGTTACTCCGCTGCGGCCGCTAG...

CDS

Download CDS FASTA

1521 bp · LXL04_039364|LXL04_039364|OH1004|CDS

ATGGCGAATCAGCTGTACGGTTCCAGCTCCTACGGGTATGGGGGAGGATCCAATTCGTCAAGCATATACACTTCTAAATCCATCGGTGAGCAGTACGTCCCCTCGGACCCATCGCACCTCACTTCGTCTAGGTATTTAGGCTCAGATCCCCTGTCAGCGTCTTCCAATTTGTTCAGCTTTTCATCAATCAGCGACAGAGCTCCATCCATGCTGTACAACCAGGATACTATCGGCAGTGGTTACTCCGCTGCGGCCGCTAG...

Protein

Download Protein FASTA

506 aa · LXL04_039364|LXL04_039364|OH1004|PROTEIN

MANQLYGSSSYGYGGGSNSSSIYTSKSIGEQYVPSDPSHLTSSRYLGSDPLSASSNLFSFSSISDRAPSMLYNQDTIGSGYSAAAARLAGREALWSGPPGVDAGVSATSVESILAGYKRSASEALYHQSLLGYSSNPIVKRPRFESAATNSMLPVYAQRPGEKDCAHYMLTRTCKFGDSCRFDHPMWVPEGGIPDWKEVLTTSEELPERPGAPDCPYFLKTQKCKFGPRCKFNHPKDKVAPLALLENTEGAELPERPSEP...

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_039364
TK1151 IDTkA04G228680
OH-1004 IDLXL04_039364
Relationship / confidenceRbh High Identity Coverage Local Synteny Minor Chr Pair / Probable
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 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_039364
LocationJAJTUU010000010.1:4399193-4405573 (-)
DescriptionSimilar to HUA1: Zinc finger CCCH domain-containing protein 37
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g12680 Involved in flower development.
HUA1, a regulator of stamen and carpel identities in Arabidopsis, codes for a nuclear RNA binding protein.2001 · DOI: 10.1105/tpc.010201
Two RNA binding proteins, HEN4 and HUA1, act in the processing of AGAMOUS pre-mRNA in Arabidopsis thaliana.2003 · DOI: 10.1016/s1534-5807(02)00399-4
At5g16540 Zinc finger CCCH domain-containing protein 57. No verified direct reference in this release
At5g18550 Zinc finger CCCH domain-containing protein 58. No verified direct reference in this release

Rice

Reference gene IDPossible functionPapers / DOI
Os01g0616400 Zinc finger CCCH domain-containing protein 8. No verified direct reference in this release
Os01g0917400 Zinc finger CCCH domain-containing protein 12. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_039364 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0001709 cell fate determination Biological Process
GO:0006397 mRNA processing Biological Process
GO:0009908 flower development Biological Process
GO:0005634 nucleus Cellular Component
GO:0016607 nuclear speck Cellular Component
GO:0003677 DNA binding Molecular Function
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0004518 nuclease activity Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT3G12680
ath:AT5G16540
dosa:Os01g0616400
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.

Nucleus0.957
Rank 1 · LXL04_039364 · OH-1004
Cytoplasm0.107
Rank 2 · LXL04_039364 · OH-1004
Cell membrane0.018
Rank 3 · LXL04_039364 · OH-1004
Plastid0.013
Rank 4 · LXL04_039364 · OH-1004
Mitochondrion0.010
Rank 5 · LXL04_039364 · 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.

PF00642.31zf-CCCH161-186 aa
PF18345.8zf_CCCH_4165-184 aa
PF00642.31zf-CCCH211-236 aa
PF25585.2zf-CCCH_DUS3L213-234 aa
PF18345.8zf_CCCH_4215-234 aa
PF18044.8zf-CCCH_4215-235 aa
PF00642.31zf-CCCH258-283 aa
PF18345.8zf_CCCH_4262-281 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_039364PF00642.31zf-CCCH1611861.6e-55184.7
LXL04_039364PF18345.8zf_CCCH_41651842.7e-2897.9
LXL04_039364PF00642.31zf-CCCH2112361.6e-55184.7
LXL04_039364PF25585.2zf-CCCH_DUS3L2132346.7e-2484.2
LXL04_039364PF18345.8zf_CCCH_42152342.7e-2897.9
LXL04_039364PF18044.8zf-CCCH_42152357.9e-2586.8
LXL04_039364PF00642.31zf-CCCH2582831.6e-55184.7
LXL04_039364PF18345.8zf_CCCH_42622812.7e-2897.9
LXL04_039364PF00642.31zf-CCCH3273521.6e-55184.7
LXL04_039364PF25585.2zf-CCCH_DUS3L3293506.7e-2484.2
LXL04_039364PF18345.8zf_CCCH_43313502.7e-2897.9
LXL04_039364PF18044.8zf-CCCH_43313517.9e-2586.8
LXL04_039364PF00642.31zf-CCCH4094301.6e-55184.7
LXL04_039364PF18044.8zf-CCCH_44624837.9e-2586.8
LXL04_039364PF00642.31zf-CCCH4634841.6e-55184.7
LXL04_039364PF18345.8zf_CCCH_44634822.7e-2897.9

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q941Q3Arabidopsis thalianaZinc finger CCCH domain-containing protein 3754.049%Swiss-Protstrong database homology
Q8L7N8Arabidopsis thalianaZinc finger CCCH domain-containing protein 5734.954%Swiss-Protmoderate database homology
Q6NPN3Arabidopsis thalianaZinc finger CCCH domain-containing protein 5832.958%Swiss-Protmoderate database homology
Q5ZDJ6Oryza sativa subsp. japonicaZinc finger CCCH domain-containing protein 852.055%Swiss-Protstrong database homology
Q5JLB5Oryza sativa subsp. japonicaZinc finger CCCH domain-containing protein 1236.364%Swiss-Protmoderate database homology

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