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

`SmilChr03G000056`

Chromosome: Chr03 Coordinates: 532326-533356 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr03G000056`
Name	SmilChr03G000056
Description	protein TIC 20-II, chloroplastic-like
Chromosome / SeqID	Chr03 / NC_080389.1
Coordinates and Strand	532326 - 533356 / `-`

ID Mapping

NCBI Gene ID	`LOC131016948`
GeneID	`131016948`
locus_tag	`-`
NCBI Name	`LOC131016948`
Original query	`SmilChr03G000056`

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Functional Annotation

Source	GFF basic annotation; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	protein TIC 20-II, chloroplastic-like
Product	protein TIC 20-II%2C chloroplastic-like
Arabidopsis	`AT2G47840` (Tic20-II) putative conserved protein ycf60 [Source:NCBI gene (formerly Entrezgene);Acc:819396] identity=51.3; qcov=0.825; evalue=2.5e-46; confidence=medium
Rice	`Os02g0726600` - identity=38.1; qcov=0.607; evalue=2.5e-11; confidence=low
GO	-
KEGG	-
Pfam	PF16166 (TIC20)
InterPro	-
eggNOG	-
NR	GeneID:131016948

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Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Chloroplast	叶绿体	1.00000	`XP_057801763.1`
2	Chloroplast membrane	叶绿体膜	1.00000	`XP_057801763.1`
3	Chloroplast thylakoid	类囊体	0.80000	`XP_057801763.1`
4	Chloroplast thylakoid membrane	类囊体膜	0.40000	`XP_057801763.1`
5	Nucleus	细胞核	0.00000	`XP_057801763.1`

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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
`Chr3:532514`	`ACT`	`A`	2bp_deletion	frameshift_variant	3	B131,B140,D3
`Chr3:532564`	`CA`	`C`	1bp_deletion	frameshift_variant	3	B54,B99,C58
`Chr3:532564`	`CA`	`C`	1bp_deletion	CDS_variant	3	B54,B99,C58
`Chr3:532607`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B126
`Chr3:532645`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B104
`Chr3:532666`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	C6
`Chr3:532688`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	C74
`Chr3:532689`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B118
`Chr3:532806`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B31
`Chr3:532878`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	C52
`Chr3:532892`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	C6
`Chr3:532992`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	B123,B42,B43

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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_057801763.1

229 aa

114

229

TIC20

PF16166 TIC20 62-200 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057801763.1`	Pfam	`PF16166`	TIC20	Family	62	200	6.8e-20	72.3	Chloroplast import apparatus Tic20-like

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_057945780.1
ATTCACTGCATTGTTAAGTAAAAAGGAACGGTGCATATTGGTTTACTCGATTATGCATGAAACCATAGGCTGCTCCTCTCTGACTCAAAAAGCATGCATTTTCATTTCCAGAGAGGGAGAGAGAGGAGAGTTGAAGACATGATGCAATTTTCATGTCCAACATTTCAATTGAAATCCCCAATTCAAAAAACCCTAAAAATCCAATCATGGCTTCCATTGCCCTCCGCCTCTCCCTCCCCAATCACTCCGCCGTCCGCCTC...

CDS

1 records

Download CDS FASTA

LOC131016948
ATGTCCAACATTTCAATTGAAATCCCCAATTCAAAAAACCCTAAAAATCCAATCATGGCTTCCATTGCCCTCCGCCTCTCCCTCCCCAATCACTCCGCCGTCCGCCTCCCTCATCCACCTCCCCAGTTCCGCCCCAAACCAACCACGACGAGGTGCTCCTACACTCCTACACCGGCGACGGAACGCCTAATCTCCGCCGCGTCCTACCTCATCCCCTTCTTCAACGGCCTCCACTACGGCCGGTTTCTGGTCGCCAAGTA...

Protein

1 records

Download Protein FASTA

XP_057801763.1
MSNISIEIPNSKNPKNPIMASIALRLSLPNHSAVRLPHPPPQFRPKPTTTRCSYTPTPATERLISAASYLIPFFNGLHYGRFLVAKYPPLAAPFEPLIRLLSRYHSVPCASFVAFLIYPCVFRNPSFSLYARSNALQALVLDLLLVLLQRITAPGWTGTGIGFNLTAWLYSGLLLFVVAGFVSSVVGNNPYLYSPIVAQPAGRRPPARIISLFCLSFFFFILFPTPKAL

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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