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

`SmilChr03G002799`

Chromosome: Chr03 Coordinates: 44482541-44486316 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr03G002799`
Name	SmilChr03G002799
Description	transcription factor bHLH130-like
Chromosome / SeqID	Chr03 / NC_080389.1
Coordinates and Strand	44482541 - 44486316 / `-`

ID Mapping

NCBI Gene ID	`LOC131015967`
GeneID	`131015967`
locus_tag	`-`
NCBI Name	`LOC131015967`
Original query	`SmilChr03G002799`

Open ID mapping

Reviewed Literature Gene-name Mapping

These entries are manually reviewed mappings between literature gene names and the current reference genome. Confidence reflects mapping evidence strength and does not mean that the reported function has been experimentally validated in this material.

Literature name	Mapping confidence	Mapping evidence	Literature function summary
`SmbHLH60`	medium	BLASTP against website protein; top hit 65.63% identity, 99% query coverage	Regulates phenolic acids and anthocyanins; antagonistic relationship with SmMYC2.

Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	transcription factor bHLH130-like
Product	transcription factor bHLH130-like
Arabidopsis	`AT2G42280` (FBH4) basic helix-loop-helix (bHLH) DNA-binding superfamily protein [Source:NCBI gene (formerly Entrezgene);Acc:818829] identity=40.1; qcov=0.924; evalue=4.99e-60; confidence=medium
Rice	`Os08g0506700` (OsFBH1) - identity=57; qcov=0.401; evalue=2.59e-49; confidence=low
GO	GO:0000978 (RNA polymerase II cis-regulatory region sequence-specific DNA binding); GO:0000981 (DNA-binding transcription factor activity, RNA polymerase II-specific); GO:0005634 (nucleus); GO:0006357 (regulation of transcription by RNA polymerase II); GO:0046983 (protein dimerization activity)
KEGG	-
Pfam	PF00010 (HLH)
InterPro	-
eggNOG	-
NR	GeneID:131015967

Open annotation module

Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Nucleus	细胞核	1.00000	`XP_057800465.1`
2	Chromosome	染色体	0.00000	`XP_057800465.1`
3	Centromere	着丝粒	0.00000	`XP_057800465.1`
4	Chromatin	染色质	0.00000	`XP_057800465.1`
5	Telomere	端粒	0.00000	`XP_057800465.1`

Open subcellular search

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
`Chr3:44483970`	`G`	`A`	EMS_canonical_SNV	stop_gained	2	B122,B33
`Chr3:44483970`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	B122,B33
`Chr3:44484007`	`C`	`T`	EMS_canonical_SNV	stop_gained	2	B108,C23
`Chr3:44484007`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B108,C23
`Chr3:44484059`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B118,C6
`Chr3:44484222`	`C`	`T`	EMS_canonical_SNV	CDS_variant	5	B115,B13,B59,C19,C3
`Chr3:44484224`	`C`	`CTT`	2bp_insertion	frameshift_variant	1	C55
`Chr3:44484224`	`C`	`CTT`	2bp_insertion	CDS_variant	1	C55
`Chr3:44484258`	`G`	`A`	EMS_canonical_SNV	CDS_variant	4	A16,B123,B77,C48
`Chr3:44484309`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B35
`Chr3:44484323`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B65
`Chr3:44484439`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	B118,C6

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_057800466.1

400 aa

200

400

HLH

PF00010 HLH 323-368 aa

XP_057800467.1

394 aa

197

394

HLH

PF00010 HLH 323-368 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057800466.1`	Pfam	`PF00010`	HLH	Domain	323	368	1.3e-08	35.2	Helix-loop-helix DNA-binding domain
`XP_057800467.1`	Pfam	`PF00010`	HLH	Domain	323	368	1.4e-08	35.1	Helix-loop-helix DNA-binding domain

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

4 records

Download cDNA FASTA

XR_009098806.1
CGCACAACAAAGACCGGATGCAACGCACCAATTCGACAATTTGACCTTTCACGTGTTGAATTCGATAATTCCGTCGCCCTATATATACCACATGTGCCTCACCCGCACTTCACCGCAACTTCCCTTTTCGTCTGTCGACAGCATTCAATCTCATTTCCTTTTTCAAGAAACAATCCCATATCCTTTGAATCCACTGCTTCTCGGAGTTTCCATTAATGTTCTCCGCCACCTTCCACACATAGAAACCTAGTCTTCTCTAG...

XM_057944484.1
TTTAAAAAAAATGATGAGATGACGTGGAGCGAGTGACATGGCAAATGGATATATACGCGTAAAATGGGAGTCATTTTTAGTCTCGCACAACAAAGACCGGATGCAACGCACCAATTCGACAATTTGACCTTTCACGTGTTGAATTCGATAATTCCGTCGCCCTATATATACCACATGTGCCTCACCCGCACTTCACCGCAACTTCCCTTTTCGTCTGTCGACAGCATTCAATCTCATTTCCTTTTTCAAGAAACAATCCC...

CDS

3 records

Download CDS FASTA

LOC131015967
ATGTTCAGCTCAGACACCATCTCCAGAGACTTCCTTCACTCCAATGCCAATCCCTCTCACCACACCAATTTCAAGCATGTCTCAGCTGATGCCGAATTCTCAAAGAGCAGAGAATTCATGCCCTCGGATTTCTTCAACAATCAGCAGCAGCACAGCTCCGGACTAGCTCGATATCGGTCGGCGCCGAGCTCGTTGTTCGCGGCCCTTCTGGATTCCAACACCGATAACAACAGCAGCAGCGGCGATGAATCAGACGCTTT...

Protein

3 records

Download Protein FASTA

XP_057800465.1
MFSSDTISRDFLHSNANPSHHTNFKHVSADAEFSKSREFMPSDFFNNQQQHSSGLARYRSAPSSLFAALLDSNTDNNSSSGDESDAFFSALIERDLNPKSSDHQISSGMKREDGAEADPRPAQNGYDAVTGSYSVGMEHHVDLRLRDENGNRSNLLRQSSSPAGFFNGFGVMGEAGDYRVPNPAEDSSSVGGLSSSMNLTSAASSSSRFMPSIPETGNQDAFSPENGRLRNEPTFQHDSWNETSFNSLKRNRDGDSKMFS...

XP_057800466.1
MFSSDTISRDFLHSNANPSHHTNFKHVSADAEFSKSREFMPSDFFNNQQQHSSGLARYRSAPSSLFAALLDSNTDNNSSSGDESDAFFSALIERDLNPKSSDHQISSGMKREDGAEADPRPAQNGYDAVTGSYSVGMEHHVDLRLRDENGNRSNLLRQSSSPAGFFNGFGVMGEAGDYRVPNPAEDSSSVGGLSSSMNLTSAASSSSRFMPSIPETGNQDAFSPENGRLRNEPTFQHDSWNETSFNSLKRNRDGDSKMFS...

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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