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

`SmilChr04G001109`

Chromosome: Chr04 Coordinates: 15924231-15929789 Strand: + Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr04G001109`
Name	SmilChr04G001109
Description	B3 domain-containing transcription repressor VAL2-like
Chromosome / SeqID	Chr04 / NC_080390.1
Coordinates and Strand	15924231 - 15929789 / `+`

ID Mapping

NCBI Gene ID	`LOC131019832`
GeneID	`131019832`
locus_tag	`-`
NCBI Name	`LOC131019832`
Original query	`SmilChr04G001109`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	B3 domain-containing transcription repressor VAL2-like
Product	B3 domain-containing transcription repressor VAL2-like
Arabidopsis	`AT4G32010` (HSL1) HSI2-like 1 [Source:NCBI gene (formerly Entrezgene);Acc:829332] identity=50.6; qcov=0.901; evalue=0; confidence=high
Rice	`Os07g0679700` (OsVAL2) - identity=50.7; qcov=0.971; evalue=0; confidence=high
GO	GO:0003677 (DNA binding); GO:0008270 (zinc ion binding)
KEGG	-
Pfam	PF02362 (B3); PF07496 (zf-CW); PF25813 (zf_VAL1_N)
InterPro	-
eggNOG	-
NR	GeneID:131019832

Open annotation module

Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Nucleus	细胞核	1.00000	`XP_057804424.1`
2	Chromosome	染色体	0.00000	`XP_057804424.1`
3	Centromere	着丝粒	0.00000	`XP_057804424.1`
4	Chromatin	染色质	0.00000	`XP_057804424.1`
5	Telomere	端粒	0.00000	`XP_057804424.1`

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
`Chr4:15925190`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	A14,B64
`Chr4:15925898`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	B52,C29
`Chr4:15926040`	`C`	`T`	EMS_canonical_SNV	CDS_variant	4	B26,B61,B8,C58
`Chr4:15926064`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B72,C21
`Chr4:15926066`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	C17
`Chr4:15926090`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	C46,C9
`Chr4:15926099`	`GC`	`G`	1bp_deletion	frameshift_variant	1	C64
`Chr4:15926099`	`GC`	`G`	1bp_deletion	CDS_variant	1	C64
`Chr4:15926340`	`C`	`T`	EMS_canonical_SNV	stop_gained	22	A15,A21,B104,B106,B119,B123,B134,B140,B2,B22,B33,B41,B47,B57,B76,B87,C13,C21,C24,C46,C50,C9
`Chr4:15926361`	`C`	`T`	EMS_canonical_SNV	CDS_variant	5	A8,B21,B35,B41,D6
`Chr4:15926409`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	A11,B17
`Chr4:15926433`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	B33,B68,C48

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_057804424.1

880 aa

440

880

zf_VAL1_N

zf-CW

PF25813 zf_VAL1_N 49-94 aa PF02362 B3 305-404 aa PF07496 zf-CW 573-615 aa

XP_057804425.1

879 aa

440

879

zf_VAL1_N

zf-CW

PF25813 zf_VAL1_N 49-94 aa PF02362 B3 305-404 aa PF07496 zf-CW 572-614 aa

XP_057804426.1

783 aa

392

783

zf-CW

PF02362 B3 208-307 aa PF07496 zf-CW 476-518 aa

XP_057804427.1

746 aa

373

746

zf-CW

PF02362 B3 171-270 aa PF07496 zf-CW 439-481 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057804424.1`	Pfam	`PF25813`	zf_VAL1_N	Domain	49	94	3.2e-22	78.9	VAL1-like, N-terminal zinc finger domain
`XP_057804424.1`	Pfam	`PF02362`	B3	Domain	305	404	4.9e-16	59.2	B3 DNA binding domain
`XP_057804424.1`	Pfam	`PF07496`	zf-CW	Domain	573	615	1.1e-08	35.6	CW-type Zinc Finger
`XP_057804425.1`	Pfam	`PF25813`	zf_VAL1_N	Domain	49	94	3.2e-22	78.9	VAL1-like, N-terminal zinc finger domain
`XP_057804425.1`	Pfam	`PF02362`	B3	Domain	305	404	4.9e-16	59.2	B3 DNA binding domain
`XP_057804425.1`	Pfam	`PF07496`	zf-CW	Domain	572	614	1.1e-08	35.6	CW-type Zinc Finger
`XP_057804426.1`	Pfam	`PF02362`	B3	Domain	208	307	4.4e-16	59.4	B3 DNA binding domain
`XP_057804426.1`	Pfam	`PF07496`	zf-CW	Domain	476	518	4.2e-09	37.0	CW-type Zinc Finger
`XP_057804427.1`	Pfam	`PF02362`	B3	Domain	171	270	4e-16	59.5	B3 DNA binding domain
`XP_057804427.1`	Pfam	`PF07496`	zf-CW	Domain	439	481	4.3e-09	37.0	CW-type Zinc Finger

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

XM_057948441.1
AAGGCAATGATGATTGCTTCAACACAAAAACAGAGAGTGCGAAAGCGTTTTCTCATTTCTGGACTTGAATTACAAACATCCGCCGCATTCCCTTTCTCTAGCCTCGTCAGCCTTCCTTCCTCACCCCCTCAACTGCGGCGCCGCGCCACTCATCCCCGCCGGCGACTAGCAGCAGGCCGACGCAGCAGCAGCAGACCAGCGCCACTGCCGGCTTCTCCTCCGCCGCCAAGATTGACGACGGCGCCGACTAGCAGCAGACC...

XM_057948442.1
AAGGCAATGATGATTGCTTCAACACAAAAACAGAGAGTGCGAAAGCGTTTTCTCATTTCTGGACTTGAATTACAAACATCCGCCGCATTCCCTTTCTCTAGCCTCGTCAGCCTTCCTTCCTCACCCCCTCAACTGCGGCGCCGCGCCACTCATCCCCGCCGGCGACTAGCAGCAGGCCGACGCAGCAGCAGCAGACCAGCGCCACTGCCGGCTTCTCCTCCGCCGCCAAGATTGACGACGGCGCCGACTAGCAGCAGACC...

CDS

4 records

Download CDS FASTA

LOC131019832
ATGGAGGGTGGAGTGTGCATGAATGGGATTTGCGGTTCATCCAGCTCGGTGGAATGGAAAAAGGGTTGGCCCTTGCGATCCGGTGGCTTTGCTACTCTCTGTCATAATTGCGGGACTGCATATAAAGATTTGGTCTTCTGCGAAACGTTCCATTCAGAGGAAACAGGTTGGAGGGAGTGCACTTCGTGTGGGAAGCGTCTTCATTGTGGATGCATTGCTTCCAGTACATTGCTGGAGCTACTCGACACTGGTGGGGTGAA...

Protein

4 records

Download Protein FASTA

XP_057804424.1
MEGGVCMNGICGSSSSVEWKKGWPLRSGGFATLCHNCGTAYKDLVFCETFHSEETGWRECTSCGKRLHCGCIASSTLLELLDTGGVNCTGCSKSCLRPYTPLEEKHKACGLSTENGTDRNSERIVPAQSGDDAKMDCQENLLPSPNANVTSRKLEDELASPEGIGYKLLSSSNQSPVGPSKNYDMFQESKSLHKSLVETNLSISLSASSNSNTLSGMMAEERQLNTAISSFQQGCRPRHLLPRVPTILAAGLETNSSSIS...

XP_057804425.1
MEGGVCMNGICGSSSSVEWKKGWPLRSGGFATLCHNCGTAYKDLVFCETFHSEETGWRECTSCGKRLHCGCIASSTLLELLDTGGVNCTGCSKSCLRPYTPLEEKHKACGLSTENGTDRNSERIVPAQSGDDAKMDCQENLLPSPNANVTSRKLEDELASPEGIGYKLLSSSNQSPVGPSKNYDMFQESKSLHKSLVETNLSISLSASSNSNTLSGMMAEERQLNTAISSFQQGCRPRHLLPRVPTILAAGLETNSSSIS...

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.

Download upstream Download downstream Download upstream + gene + downstream

JBrowse

Open genome browser