Gene Card

Search by standard ID, NCBI Gene ID, GeneID, locus tag, transcript ID, protein ID, or a manually reviewed literature gene name. The page resolves the query to a Red Sage gene and integrates coordinates, sequences, annotations, subcellular localization, EMS variants, and downloads.

Resolved gene

`SmilChr03G004141`

Chromosome: Chr03 Coordinates: 60243987-60245499 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr03G004141`
Name	SmilChr03G004141
Description	zinc finger protein CONSTANS-LIKE 4-like
Chromosome / SeqID	Chr03 / NC_080389.1
Coordinates and Strand	60243987 - 60245499 / `-`

ID Mapping

NCBI Gene ID	`LOC131015006`
GeneID	`131015006`
locus_tag	`-`
NCBI Name	`LOC131015006`
Original query	`SmilChr03G004141`

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Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	zinc finger protein CONSTANS-LIKE 4-like
Product	zinc finger protein CONSTANS-LIKE 4-like
Arabidopsis	`AT5G24930` (COL4) zinc finger CONSTANS-like protein [Source:NCBI gene (formerly Entrezgene);Acc:832563] identity=50.7; qcov=1.11; evalue=7.2e-96; confidence=high
Rice	`Os04g0497700` (OsBBX12) - identity=45; qcov=0.976; evalue=7.02e-67; confidence=medium
GO	GO:0005515 (protein binding); GO:0005634 (nucleus); GO:0008270 (zinc ion binding); GO:0009909 (regulation of flower development); GO:2000028 (regulation of photoperiodism, flowering)
KEGG	-
Pfam	PF00643 (zf-B_box); PF06203 (CCT)
InterPro	-
eggNOG	-
NR	GeneID:131015006

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Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Nucleus	细胞核	1.00000	`XP_057799183.1`
2	Chromosome	染色体	0.00000	`XP_057799183.1`
3	Centromere	着丝粒	0.00000	`XP_057799183.1`
4	Chromatin	染色质	0.00000	`XP_057799183.1`
5	Telomere	端粒	0.00000	`XP_057799183.1`

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EMS Mutant Variants

The table shows the first 12 candidate EMS variants for this gene. Open the EMS module for full filtering and downloads.

Position	REF	ALT	Type	Effect	Carriers	Samples
`Chr3:60244216`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	B90,B92
`Chr3:60244413`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	C13
`Chr3:60244609`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B123
`Chr3:60244647`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B35
`Chr3:60244775`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B101
`Chr3:60244849`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	A22
`Chr3:60244924`	`C`	`T`	EMS_canonical_SNV	CDS_variant	4	B38,B39,C77,D7
`Chr3:60244945`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	C43,D4
`Chr3:60244954`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	C43

Open EMS variants

Predicted Protein Domains

Domain results are from the Pfam-A HMM database and HMMER hmmscan; positions are amino-acid coordinates on the corresponding protein sequence.

XP_057799183.1

335 aa

168

335

zf-B_box

CCT

PF00643 zf-B_box 11-42 aa PF00643 zf-B_box 53-98 aa PF06203 CCT 271-312 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057799183.1`	Pfam	`PF00643`	zf-B_box	Domain	11	42	4.4e-15	56.3	B-box zinc finger
`XP_057799183.1`	Pfam	`PF00643`	zf-B_box	Domain	53	98	4.4e-15	56.3	B-box zinc finger
`XP_057799183.1`	Pfam	`PF06203`	CCT	Motif	271	312	4.3e-18	65.8	CCT motif

cDNA / CDS / Protein Sequences

Download genomic DNA (gene region only)

Every public gene has transcript sequence from the reference annotation. Protein-coding genes also have CDS and protein sequences. CDS and protein downloads do not apply to noncoding RNA. Version suffixes of original accessions are retained.

cDNA

1 records

Download cDNA FASTA

XM_057943200.1
TTTTTTATTTGGCTAAGAGTCGGCCATATGTCGTCACCTGATTGGCTATCCCCGAGATCATCCCTACCCATTCAGCTCACTTTACAAACACTTCCCACTATACACACTGCACTTCATAAAAACTCAAACAAGTTTGCAATTATCTCTTAAATTTCTTCATCTAGAGAGAGAGAGAGAAATTAAGGCGGGAGGCAAAAAAACACAGAGAGAGAGAAGAAACAAATGGGGGCGGAAACCTGGAGCCTAACCGCGAAGCTCTG...

CDS

1 records

Download CDS FASTA

LOC131015006
ATGGGGGCGGAAACCTGGAGCCTAACCGCGAAGCTCTGCGACTCGTGCAAGGCGGCGCCCGCGGCCGTCTTCTGCCGCGCTGACTCGGCGTTCCTGTGCGGCGCGTGCGACGGCAAGATCCACGCCGCCAACAAGCTGGCGTCGCGCCACGGCCGCGTCTGGATCTGCGAGGTGTGCGAGCAGGCCCCGGCCTCCTTCACCTGCAAGGCCGACGCCGCCTCCCTCTGCGCCGCCTGCGACCGCGACATCCACTCCGCCAA...

Protein

1 records

Download Protein FASTA

XP_057799183.1
MGAETWSLTAKLCDSCKAAPAAVFCRADSAFLCGACDGKIHAANKLASRHGRVWICEVCEQAPASFTCKADAASLCAACDRDIHSANPLARRHERVPVVPFYDSAAKSSPSAECSEEEAEAASWLLPDPNSKVEEEESGSPEYMSAEYLFNDMDPYLDLDLKSGDQKPHHIVDDDHKHYSSDGVVPVQSKTEYGSGHYVPGPVVDGFPTYEMEYPGPKPFMYNFTSQSISQSVSSSSLEVGVVPDHNGAADATESLGKSE...

Flanking Sequence Downloads

Upstream/downstream length is capped at 10000 bp. Negative-strand genes are reverse-complemented so the exported FASTA follows transcriptional 5′ to 3′ orientation.

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