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

`SmilChr02G002187`

Chromosome: Chr02 Coordinates: 39074556-39076521 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr02G002187`
Name	SmilChr02G002187
Description	zinc finger BED domain-containing protein RICESLEEPER 2-like
Chromosome / SeqID	Chr02 / NC_080388.1
Coordinates and Strand	39074556 - 39076521 / `-`

ID Mapping

NCBI Gene ID	`LOC131012376`
GeneID	`131012376`
locus_tag	`-`
NCBI Name	`LOC131012376`
Original query	`SmilChr02G002187`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	zinc finger BED domain-containing protein RICESLEEPER 2-like
Product	zinc finger BED domain-containing protein RICESLEEPER 2-like
Arabidopsis	`AT3G42170` (DAYSLEEPER) BED zinc finger and hAT dimerization domain-containing protein DAYSLEEPER [Source:NCBI gene (formerly Entrezgene);Acc:3769417] identity=36.5; qcov=0.964; evalue=2.47e-63; confidence=medium
Rice	`Os05g0583100` - identity=38.2; qcov=1; evalue=4.38e-76; confidence=medium
GO	GO:0003677 (DNA binding); GO:0046983 (protein dimerization activity)
KEGG	-
Pfam	PF05699 (Dimer_Tnp_hAT); PF14372 (hAT-like_RNase-H); PF27039 (ZBED1_RNase-like_helical)
InterPro	-
eggNOG	-
NR	GeneID:131012376

Open annotation module

Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Nucleus	细胞核	1.00000	`XP_057796287.1`
2	Cytoplasm	细胞质	0.20000	`XP_057796287.1`
3	Chromosome	染色体	0.00000	`XP_057796287.1`
4	Centromere	着丝粒	0.00000	`XP_057796287.1`
5	Chromatin	染色质	0.00000	`XP_057796287.1`

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
`Chr2:39075448`	`G`	`A`	EMS_canonical_SNV	CDS_variant	4	A2,B93,C53,D2
`Chr2:39075465`	`C`	`T`	EMS_canonical_SNV	CDS_variant	5	B26,B36,B58,C35,C51
`Chr2:39075474`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	B26,B30,C51
`Chr2:39075504`	`C`	`T`	EMS_canonical_SNV	CDS_variant	5	A13,B26,B51,C15,C57
`Chr2:39075510`	`GC`	`G`	1bp_deletion	frameshift_variant	194	A1,A10,A11,A14,A15,A19,A2,A20,A21,A23,A4,A5,A6,A7,A8,A9,B10,B101,B102,B104,B105,B106,B108,B109,B111,B112,B114,B115,B117,B118,B119,B12,B120,B121,B123,B126,B128,B130,B131,B132,B133,B134,B136,B137,B139,B14,B140,B15,B16,B18,B2,B20,B21,B22,B23,B24,B25,B26,B27,B28,B29,B3,B32,B33,B34,B35,B36,B37,B38,B39,B4,B41,B42,B43,B44,B45,B46,B47,B48,B49,B5,B50,B51,B52,B53,B54,B55,B57,B58,B59,B6,B60,B62,B63,B64,B65,B66,B67,B68,B70,B72,B73,B75,B79,B80,B82,B83,B84,B85,B86,B88,B89,B9,B91,B92,B93,B94,B95,B96,B97,B98,C11,C12,C13,C14,C16,C17,C18,C19,C2,C20,C21,C23,C24,C25,C26,C27,C28,C29,C3,C30,C32,C33,C34,C35,C36,C38,C4,C40,C41,C43,C44,C45,C46,C47,C48,C49,C50,C52,C55,C56,C57,C58,C6,C61,C63,C68,C69,C7,C71,C73,C74,C75,C76,C77,C78,C79,C8,C80,C81,C82,C84,C85,C86,C87,C9,D1,D11,D3,D4,D5,D6,D8,D9
`Chr2:39075522`	`C`	`T`	EMS_canonical_SNV	CDS_variant	3	B118,B126,B2
`Chr2:39075523`	`G`	`A`	EMS_canonical_SNV	stop_gained	66	A10,A23,A7,A8,B101,B102,B109,B110,B117,B118,B12,B121,B131,B137,B16,B21,B24,B28,B3,B36,B38,B39,B44,B45,B48,B50,B53,B54,B6,B62,B64,B67,B68,B8,B88,B9,B93,C12,C14,C16,C17,C2,C22,C24,C25,C26,C32,C34,C35,C4,C40,C41,C43,C46,C58,C63,C67,C68,C7,C77,C79,C81,C82,C84,C85,D8
`Chr2:39075554`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	A23,C54
`Chr2:39075588`	`GC`	`G`	1bp_deletion	frameshift_variant	12	A13,A3,B114,B130,B22,B56,B96,C15,C53,C59,C60,D10
`Chr2:39075621`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B42,B43
`Chr2:39075646`	`CAA`	`C`	2bp_deletion	frameshift_variant	5	A13,B2,B58,C15,C57
`Chr2:39075646`	`CAA`	`C`	2bp_deletion	CDS_variant	5	A13,B2,B58,C15,C57

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_057796287.1

373 aa

186

373

ZBED1_RNase-like_helical

hAT-like_RNase-H

Dimer_Tnp_hAT

PF27039 ZBED1_RNase-like_helical 1-99 aa PF14372 hAT-like_RNase-H 120-214 aa PF05699 Dimer_Tnp_hAT 264-348 aa

XP_057796288.1

364 aa

182

364

ZBED1_RNase-like_helical

hAT-like_RNase-H

Dimer_Tnp_hAT

PF27039 ZBED1_RNase-like_helical 1-99 aa PF14372 hAT-like_RNase-H 120-214 aa PF05699 Dimer_Tnp_hAT 264-348 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057796287.1`	Pfam	`PF27039`	ZBED1_RNase-like_helical	Domain	1	99	4.4e-24	85.4	ZBED1 RNase-like helical domain
`XP_057796287.1`	Pfam	`PF14372`	hAT-like_RNase-H	Domain	120	214	6.7e-30	103.9	hAT-like transposase, RNase-H fold
`XP_057796287.1`	Pfam	`PF05699`	Dimer_Tnp_hAT	Domain	264	348	3.4e-24	85.1	hAT family C-terminal dimerisation region
`XP_057796288.1`	Pfam	`PF27039`	ZBED1_RNase-like_helical	Domain	1	99	4.2e-24	85.4	ZBED1 RNase-like helical domain
`XP_057796288.1`	Pfam	`PF14372`	hAT-like_RNase-H	Domain	120	214	6.3e-30	104.0	hAT-like transposase, RNase-H fold
`XP_057796288.1`	Pfam	`PF05699`	Dimer_Tnp_hAT	Domain	264	348	3.3e-24	85.2	hAT family C-terminal dimerisation region

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

3 records

Download cDNA FASTA

XR_009097305.1
GTGCACACATCCTGAACCTTATGGTTCAGGAAGGACTTTCAAGGATTGCTTACATTATTGAAGACATACATGAAAGTGTGCTCTTCATCAATTACAATGAGGCAAGACTTCGAGCATTCTCTGAAATTGTGCAGCAGTTACAACTACCACATCGGAAGCTTGTTCTCGAGTGCAAAACAAGATGGAATTCCACATATGAAATGCTGTCATCTGCCATCTTGTTCAAAGAGGTGTTCCCAAGATATCAAGATAGAGAGCCA...

XM_057940305.1
GGTGTTGTGCACACATCCTGAACCTTATGGTTCAGGAAGGACTTTCAAGGATTGCTTACATTATTGAAGACATACATGAAAGTGTGCTCTTCATCAATTACAATGAGGCAAGACTTCGAGCATTCTCTGAAATTGTGCAGCAGTTACAACTACCACATCGGAAGCTTGTTCTCGAGTGCAAAACAAGATGGAATTCCACATATGAAATGCTGTCATCTGCCATCTTGTTCAAAGAGGTGTTCCCAAGATATCAAGATAGA...

CDS

2 records

Download CDS FASTA

LOC131012376
ATGGTTCAGGAAGGACTTTCAAGGATTGCTTACATTATTGAAGACATACATGAAAGTGTGCTCTTCATCAATTACAATGAGGCAAGACTTCGAGCATTCTCTGAAATTGTGCAGCAGTTACAACTACCACATCGGAAGCTTGTTCTCGAGTGCAAAACAAGATGGAATTCCACATATGAAATGCTGTCATCTGCCATCTTGTTCAAAGAGGTGTTCCCAAGATATCAAGATAGAGAGCCACGATATACTTGTTGTCCAAG...

Protein

2 records

Download Protein FASTA

XP_057796287.1
MVQEGLSRIAYIIEDIHESVLFINYNEARLRAFSEIVQQLQLPHRKLVLECKTRWNSTYEMLSSAILFKEVFPRYQDREPRYTCCPSNEDWVMVEKVCTILEVFDSATRIISGSEYPTSNLFLNEVYRIKVLLDKLHGDETEAPFIHDMVGAMKTKFDKYWGECNLLMAIAAILDPRCKMTVIEYCFPKMYSKEEAREKIKKVKDALYELYDEYVADMYSDTSTQSEQIIDNTDRRSGVKVASGWSEFIQHVKSAQTSKP...

XP_057796288.1
MVQEGLSRIAYIIEDIHESVLFINYNEARLRAFSEIVQQLQLPHRKLVLECKTRWNSTYEMLSSAILFKEVFPRYQDREPRYTCCPSNEDWVMVEKVCTILEVFDSATRIISGSEYPTSNLFLNEVYRIKVLLDKLHGDETEAPFIHDMVGAMKTKFDKYWGECNLLMAIAAILDPRCKMTVIEYCFPKMYSKEEAREKIKKVKDALYELYDEYVADMYSDTSTQSEQIIDNTDRRSGVKVASGWSEFIQHVKSAQTSKP...

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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