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

`SmilChr03G000196`

Chromosome: Chr03 Coordinates: 2222923-2228958 Strand: + Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr03G000196`
Name	SmilChr03G000196
Description	uncharacterized SmilChr03G000196
Chromosome / SeqID	Chr03 / NC_080389.1
Coordinates and Strand	2222923 - 2228958 / `+`

ID Mapping

NCBI Gene ID	`LOC131016846`
GeneID	`131016846`
locus_tag	`-`
NCBI Name	`LOC131016846`
Original query	`SmilChr03G000196`

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Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	LETM1-like protein [Source:NCBI gene (formerly Entrezgene);Acc:842865]; symbol=LETM2; hit=AT1G65540; species=arabidopsis; confidence=high
Product	LETM1-like protein [Source:NCBI gene (formerly Entrezgene);Acc:842865]; symbol=LETM2; hit=AT1G65540; species=arabidopsis; confidence=high
Arabidopsis	`AT1G65540` (LETM2) LETM1-like protein [Source:NCBI gene (formerly Entrezgene);Acc:842865] identity=75.8; qcov=0.865; evalue=0; confidence=high
Rice	`Os04g0496800` - identity=71.2; qcov=0.879; evalue=0; confidence=high
GO	GO:0005509 (calcium ion binding); GO:0005743 (mitochondrial inner membrane); GO:0030003 (intracellular monoatomic cation homeostasis); GO:0043022 (ribosome binding)
KEGG	-
Pfam	PF07766 (LETM1_RBD); PF13499 (EF-hand_7)
InterPro	-
eggNOG	-
NR	GeneID:131016846

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Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Mitochondrion	线粒体	1.00000	`XP_057801601.1`
2	Mitochondrion membrane	线粒体膜	1.00000	`XP_057801601.1`
3	Mitochondrion inner membrane	线粒体内膜	1.00000	`XP_057801601.1`
4	Nucleus	细胞核	0.00000	`XP_057801601.1`
5	Chromosome	染色体	0.00000	`XP_057801601.1`

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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
`Chr3:2223517`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B91
`Chr3:2223567`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	C32,C68
`Chr3:2223589`	`C`	`T`	EMS_canonical_SNV	CDS_variant	4	A14,B24,B8,C33
`Chr3:2223594`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B104
`Chr3:2223604`	`CTG`	`C`	2bp_deletion	frameshift_variant	1	C71
`Chr3:2223604`	`CTG`	`C`	2bp_deletion	CDS_variant	1	C71
`Chr3:2223607`	`AT`	`A`	1bp_deletion	frameshift_variant	1	C71
`Chr3:2223607`	`AT`	`A`	1bp_deletion	CDS_variant	1	C71
`Chr3:2223614`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B30,B67
`Chr3:2223627`	`C`	`T`	EMS_canonical_SNV	CDS_variant	3	B65,C20,C6
`Chr3:2223690`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	A5,B62,B75
`Chr3:2223695`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	D10

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_057801601.1

735 aa

368

735

LETM1_RBD

EF-hand_7

PF07766 LETM1_RBD 223-455 aa PF13499 EF-hand_7 659-721 aa

XP_057801602.1

735 aa

368

735

LETM1_RBD

EF-hand_7

PF07766 LETM1_RBD 223-455 aa PF13499 EF-hand_7 659-721 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057801601.1`	Pfam	`PF07766`	LETM1_RBD	Domain	223	455	2.5e-86	289.7	LETM1-like, RBD
`XP_057801601.1`	Pfam	`PF13499`	EF-hand_7	Domain	659	721	2.1e-08	35.1	EF-hand domain pair
`XP_057801602.1`	Pfam	`PF07766`	LETM1_RBD	Domain	223	455	2.5e-86	289.7	LETM1-like, RBD
`XP_057801602.1`	Pfam	`PF13499`	EF-hand_7	Domain	659	721	2.1e-08	35.1	EF-hand domain pair

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

2 records

Download cDNA FASTA

XM_057945619.1
GCTCGTATTTTGTTGGATGCACACTGATCCGCCGCAGCTGATAACTCCATACCCGTTTTCATGCTCCAAGCACAATCGAGCTTCTATAGCGCTCCAAATCTCTACCAAAATTCTGATTAAAAAAATACGTAGAGAGAATCAAAGAGGACTTGCAATTTTCGTTCGCATTTCTTCGCTCATTCTCGGTCGATTGTCTCGTGCATTGCGAGTTTGAAATTCACAATCGTGAAACTGCCAGTTATCAGAATTGTTGGAATGTG...

XM_057945618.1
CGAGCTTCTATAGCGCTCCAAATCTCTACCAAAATTCTGATTAAAAAAATACGTAGAGAGAATCAAAGAGGACTTGCAATTTTCGTTCGCATTTCTTCGCTCATTCTCGGTCGATTGTCTCGTGCATTGCGAGGTCGGGATTTTTCATTGATTTTTCCTCTCAGAATAATCCACTTTTTACTTCTATTTTCAGAATTTATGTTTGAAATTCACAATCGTGAAACTGCCAGTTATCAGAATTGTTGGAATGTGCTGCGATA...

CDS

2 records

Download CDS FASTA

LOC131016846
ATGATGGCTTCAAGAGCAATATTGCAAAAGAAAAAGTGTCTGCTTGATTCATTCAAGCGGCCACATTATTTAGTTCAAAGGCTCGTATGTAGTGACCATGGAAGATTGCTAGACATTCCCGATTCACAGCGTGGGAGTTGGCCTCTGATTCTTTCGGATTCAGATAACAGAGAGAAACAACATTCATATTTTCTAACCAGACAAATGGCTCAACACACTCCGACAAAAAAGTATGCGAGTTTGCACCGTGAGATTGGAGT...

Protein

2 records

Download Protein FASTA

XP_057801601.1
MMASRAILQKKKCLLDSFKRPHYLVQRLVCSDHGRLLDIPDSQRGSWPLILSDSDNREKQHSYFLTRQMAQHTPTKKYASLHREIGVCHLSTAPAGKPELEGDDNKKEPVKQKKDPSPEECDQAVEGLSSVKAKAKAKAKQLQDSSKGVKYIVKKIRAFLLGIGPALRAIASMSWEDWANKLRHWKDEFKSTLQHYWLGTKLLWVDVRISLRLLLKLGSGRTLSRRERQQLTRTTADIFRLVPFAVFVLVPFMEFLLPAF...

XP_057801602.1
MMASRAILQKKKCLLDSFKRPHYLVQRLVCSDHGRLLDIPDSQRGSWPLILSDSDNREKQHSYFLTRQMAQHTPTKKYASLHREIGVCHLSTAPAGKPELEGDDNKKEPVKQKKDPSPEECDQAVEGLSSVKAKAKAKAKQLQDSSKGVKYIVKKIRAFLLGIGPALRAIASMSWEDWANKLRHWKDEFKSTLQHYWLGTKLLWVDVRISLRLLLKLGSGRTLSRRERQQLTRTTADIFRLVPFAVFVLVPFMEFLLPAF...

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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