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

`SmilChr08G004336`

Chromosome: Chr08 Coordinates: 53017363-53023826 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr08G004336`
Name	SmilChr08G004336
Description	zinc finger CCCH domain-containing protein 56-like
Chromosome / SeqID	Chr08 / NC_080394.1
Coordinates and Strand	53017363 - 53023826 / `-`

ID Mapping

NCBI Gene ID	`LOC130999063`
GeneID	`130999063`
locus_tag	`-`
NCBI Name	`LOC130999063`
Original query	`SmilChr08G004336`

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Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	zinc finger CCCH domain-containing protein 56-like
Product	zinc finger CCCH domain-containing protein 56-like
Arabidopsis	`AT1G32360` (AT1G32360) Zinc finger (CCCH-type) family protein [Source:NCBI gene (formerly Entrezgene);Acc:840128] identity=36.6; qcov=1.01; evalue=4.22e-53; confidence=medium
Rice	`Os08g0159800` (OsC3H56) - identity=36.1; qcov=0.978; evalue=2.21e-56; confidence=medium
GO	GO:0003729 (mRNA binding); GO:0046872 (metal ion binding)
KEGG	-
Pfam	PF00642 (zf-CCCH)
InterPro	-
eggNOG	-
NR	GeneID:130999063

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Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Nucleus	细胞核	1.00000	`XP_057780512.1`
2	Chromosome	染色体	0.00000	`XP_057780512.1`
3	Centromere	着丝粒	0.00000	`XP_057780512.1`
4	Chromatin	染色质	0.00000	`XP_057780512.1`
5	Telomere	端粒	0.00000	`XP_057780512.1`

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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
`Chr8:53017626`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B123
`Chr8:53017667`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B122
`Chr8:53017668`	`G`	`A`	EMS_canonical_SNV	CDS_variant	4	B76,B83,C46,C86
`Chr8:53017790`	`C`	`T`	EMS_canonical_SNV	CDS_variant	4	B40,B5,C33,C61
`Chr8:53021051`	`G`	`A`	EMS_canonical_SNV	CDS_variant	4	A19,A8,B35,D2
`Chr8:53021449`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	C41
`Chr8:53021660`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	D3
`Chr8:53021673`	`G`	`A`	EMS_canonical_SNV	CDS_variant	5	A19,A8,B35,B53,C8
`Chr8:53021706`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B123

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_057780512.1

323 aa

162

323

zf-CCCH

PF00642 zf-CCCH 213-238 aa

XP_057780513.1

323 aa

162

323

zf-CCCH

PF00642 zf-CCCH 213-238 aa

XP_057780514.1

323 aa

162

323

zf-CCCH

PF00642 zf-CCCH 213-238 aa

XP_057780515.1

323 aa

162

323

zf-CCCH

PF00642 zf-CCCH 213-238 aa

XP_057780516.1

323 aa

162

323

zf-CCCH

PF00642 zf-CCCH 213-238 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057780512.1`	Pfam	`PF00642`	zf-CCCH	Family	213	238	1.5e-11	44.6	Zinc finger C-x8-C-x5-C-x3-H type (and similar)
`XP_057780513.1`	Pfam	`PF00642`	zf-CCCH	Family	213	238	1.5e-11	44.6	Zinc finger C-x8-C-x5-C-x3-H type (and similar)
`XP_057780514.1`	Pfam	`PF00642`	zf-CCCH	Family	213	238	1.5e-11	44.6	Zinc finger C-x8-C-x5-C-x3-H type (and similar)
`XP_057780515.1`	Pfam	`PF00642`	zf-CCCH	Family	213	238	1.5e-11	44.6	Zinc finger C-x8-C-x5-C-x3-H type (and similar)
`XP_057780516.1`	Pfam	`PF00642`	zf-CCCH	Family	213	238	1.5e-11	44.6	Zinc finger C-x8-C-x5-C-x3-H type (and similar)

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

5 records

Download cDNA FASTA

XM_057924533.1
GAAAATATGAAAAAATATGTGAGTGATAAAAAGAGAGGTATAAACATTGCTGTGGGCCGGCGGTGGTGGTGGAGCTGCCACCGCCGCCGCCGATGAGAGTTCCAGGCACTACGCGTCGTTCGGTCGCAGTTTTCAACCGCCGGCGCGGCTGCGCCGAGGCTCTTAGAGACGATGAATAGAGGATTTTGCGATGGAAAAAGAACCTTCATTCACCAAGGTGGAGATGCAAGTATGGAAACTCGTTCCAAAATGCCAAAATG...

XM_057924532.1
ATATGAAAAAATATGTGAGTGATAAAAAGAGAGGTATAAACATTGCTGTGGGCCGGCGGTGGTGGTGGAGCTGCCACCGCCGCCGCCGATGAGAGTTCCAGGCACTACGCGTCGTTCGGTCGCAGTTTTCAACCGCCGGCGCGGCTGCGCCGAGGCTCTTAGTTCCAGTGTTATTTCATGAGTTGGTAGCAGTGACACTCTGGGTTGATGGTGCCTGATTAAGCTTAAGAGGATTTCTCTTGATTTTGTGTGGATATGGA...

CDS

5 records

Download CDS FASTA

LOC130999063
ATGGAATGTAATCGGGGGACTGGATCCCATGTGGCAAATGTAGTAGGTTTCCAATCTGGAAACCCAGGGAACAGTGCCAAGGATGGTATGTGTGAAAGAGAAACATCTGTTCACACTAATTTAACATCAAATTGTAATGAACGATCATTCCAATTTGAAGTGGAAAGTGAGCCACCAAATAAAAGAGCAAAGAATGACCTCTTGGAGGATTCGACTACCTTTGATCGCAAGAAGACCATTGGAAAGGTGCTTTACAAGAC...

Protein

5 records

Download Protein FASTA

XP_057780512.1
MECNRGTGSHVANVVGFQSGNPGNSAKDGMCERETSVHTNLTSNCNERSFQFEVESEPPNKRAKNDLLEDSTTFDRKKTIGKVLYKTRLCFQFRAGSCPFDENCDFAHSMEELRELPHNWQEILATHKEELMELSEQSRDVFQIPAEETHRPSLRQYCKGFLSRVGCQYGENCLLIHNEHYMERKSAAICLIPGPGSGFGSNGSKLTSNASHWKSRLCNKWESTGICEYGRNCVFAHGFAELQHYGGWRVKEEDIGSSAF...

XP_057780513.1
MECNRGTGSHVANVVGFQSGNPGNSAKDGMCERETSVHTNLTSNCNERSFQFEVESEPPNKRAKNDLLEDSTTFDRKKTIGKVLYKTRLCFQFRAGSCPFDENCDFAHSMEELRELPHNWQEILATHKEELMELSEQSRDVFQIPAEETHRPSLRQYCKGFLSRVGCQYGENCLLIHNEHYMERKSAAICLIPGPGSGFGSNGSKLTSNASHWKSRLCNKWESTGICEYGRNCVFAHGFAELQHYGGWRVKEEDIGSSAF...

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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