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

`SmilChr04G003114`

Chromosome: Chr04 Coordinates: 47699851-47702672 Strand: + Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr04G003114`
Name	SmilChr04G003114
Description	zinc finger protein GAI-ASSOCIATED FACTOR 1-like
Chromosome / SeqID	Chr04 / NC_080390.1
Coordinates and Strand	47699851 - 47702672 / `+`

ID Mapping

NCBI Gene ID	`LOC131023911`
GeneID	`131023911`
locus_tag	`-`
NCBI Name	`LOC131023911`
Original query	`SmilChr04G003114`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	zinc finger protein GAI-ASSOCIATED FACTOR 1-like
Product	zinc finger protein GAI-ASSOCIATED FACTOR 1-like
Arabidopsis	`AT5G66730` (IDD1) C2H2-like zinc finger protein [Source:NCBI gene (formerly Entrezgene);Acc:836806] identity=53.4; qcov=1.07; evalue=4.83e-165; confidence=high
Rice	`Os03g0197800` (OsIDD1) - identity=88; qcov=0.35; evalue=6.44e-112; confidence=low
GO	GO:0003700 (DNA-binding transcription factor activity); GO:0005634 (nucleus)
KEGG	-
Pfam	PF00096 (zf-C2H2); PF22992 (C2CH-4th_BIRD-IDD); PF22995 (C2CH-3rd_BIRD-IDD); PF22996 (C2H2-2nd_BIRD-IDD)
InterPro	-
eggNOG	-
NR	GeneID:131023911

Open annotation module

Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Nucleus	细胞核	1.00000	`XP_057809538.1`
2	Chromosome	染色体	0.00000	`XP_057809538.1`
3	Centromere	着丝粒	0.00000	`XP_057809538.1`
4	Chromatin	染色质	0.00000	`XP_057809538.1`
5	Telomere	端粒	0.00000	`XP_057809538.1`

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
`Chr4:47700653`	`ACG`	`A`	2bp_deletion	frameshift_variant	49	A14,A19,A2,B102,B104,B106,B109,B117,B119,B12,B126,B129,B13,B130,B131,B20,B22,B23,B28,B37,B4,B48,B5,B51,B60,B65,B7,B75,B76,B9,B91,C10,C19,C20,C21,C23,C37,C38,C45,C48,C6,C60,C77,C8,C83,D10,D2,D5,D9
`Chr4:47700725`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	C77,D10
`Chr4:47700761`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	C77,D10
`Chr4:47700802`	`T`	`TTA`	2bp_insertion	frameshift_variant	3	C23,C37,C38
`Chr4:47700802`	`T`	`TTA`	2bp_insertion	CDS_variant	3	C23,C37,C38
`Chr4:47700909`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B60
`Chr4:47701726`	`C`	`T`	EMS_canonical_SNV	CDS_variant	3	B13,B35,B88
`Chr4:47701774`	`C`	`T`	EMS_canonical_SNV	CDS_variant	3	B13,B35,B88
`Chr4:47701810`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B59,B86
`Chr4:47701834`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B33
`Chr4:47702101`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B59
`Chr4:47702425`	`GC`	`G`	1bp_deletion	frameshift_variant	2	B34,B43

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_057809538.1

500 aa

250

500

zf-C2H2

C2H2-2nd_BIRD-IDD

C2CH-3rd_BIRD-IDD

C2CH-4th_BIRD-IDD

PF00096 zf-C2H2 53-75 aa PF22996 C2H2-2nd_BIRD-IDD 90-124 aa PF22995 C2CH-3rd_BIRD-IDD 128-152 aa PF22992 C2CH-4th_BIRD-IDD 155-192 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057809538.1`	Pfam	`PF00096`	zf-C2H2	Domain	53	75	4.4e-09	37.0	Zinc finger, C2H2 type
`XP_057809538.1`	Pfam	`PF22996`	C2H2-2nd_BIRD-IDD	Family	90	124	3.2e-22	79.0	BIRD-IDD transcription factor, second C2H2 zinc finger
`XP_057809538.1`	Pfam	`PF22995`	C2CH-3rd_BIRD-IDD	Domain	128	152	1.1e-14	54.4	BIRD-IDD transcription factor, third C2HC zinc finger
`XP_057809538.1`	Pfam	`PF22992`	C2CH-4th_BIRD-IDD	Domain	155	192	1.3e-22	80.1	BIRD-IDD transcription factor, fourth C2HC 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

1 records

Download cDNA FASTA

XM_057953555.1
AAAATGGATGCAAATAAGCCTGAAAAAGTTAAAAGTGGGTTATGTGAAGACCAAAAAGGCAACAACGAAGACTTTTGCAAACACAGACACACACACACTCTCTCTCTCTAAAATTTCTCTCTCTAATTATCTGACTTGCCGCCGACCCTCAAAAGCCACTCTTCCTCCAGTCGGCGTGGTTCTGAACGGCGCCGCCGCAGCAGAATCAAGCTGAAATATTTCGCTGTCTAACGCGTTCGAACATGCCACCGCGCGTAGGT...

CDS

1 records

Download CDS FASTA

LOC131023911
ATGAATGAGTCGGCAGCTTCTGGCGACTCTTCTTCAGGTAATCAAACAACCCCTCCAAAACCAACTGCAAAGAAGAAACGGAATCTGCCTGGAATGCCAGATCCTGACGCCGAGGTGATTGCCCTATCGCCGAAGACGTTGATGGCGACGAATAGATTTGTGTGCGAAATCTGCAACAAAGGTTTCCAAAGGGATCAGAATCTGCAGCTGCATCGGAGGGGTCACAATCTGCCATGGAAGCTGCGGCAGAGATCGAGTAA...

Protein

1 records

Download Protein FASTA

XP_057809538.1
MNESAASGDSSSGNQTTPPKPTAKKKRNLPGMPDPDAEVIALSPKTLMATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRSSKDVKKRVYVCPEPSCVHHEPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKKYAVQSDWKAHSKICGTREYKCQCGTVFSRRDSYITHRAFCDALADESAKAPSATEPAADADQDLEAGVSSLPPPPPEEDPSPPADVAPSILPDNSNDNNSDHVTELLDSTTANPSSSQILEEL...

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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