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

`SmilChr04G000026`

Chromosome: Chr04 Coordinates: 270168-273153 Strand: + Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr04G000026`
Name	SmilChr04G000026
Description	RGG repeats nuclear RNA binding protein A-like
Chromosome / SeqID	Chr04 / NC_080390.1
Coordinates and Strand	270168 - 273153 / `+`

ID Mapping

NCBI Gene ID	`LOC131022838`
GeneID	`131022838`
locus_tag	`-`
NCBI Name	`LOC131022838`
Original query	`SmilChr04G000026`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	RGG repeats nuclear RNA binding protein A-like
Product	RGG repeats nuclear RNA binding protein A-like
Arabidopsis	`AT4G17520` (AT4G17520) Hyaluronan / mRNA binding family [Source:NCBI gene (formerly Entrezgene);Acc:827467] identity=49.6; qcov=1.06; evalue=4.43e-82; confidence=high
Rice	`Os01g0721900` (P0690B02.26-1) - identity=52.3; qcov=1.08; evalue=3.95e-60; confidence=high
GO	GO:0003723 (RNA binding); GO:0005634 (nucleus); GO:0005737 (cytoplasm)
KEGG	-
Pfam	PF04774 (HABP4_PAI-RBP1); PF09598 (Stm1_N)
InterPro	-
eggNOG	-
NR	GeneID:131022838

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Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Cytoplasm	细胞质	1.00000	`XP_057808355.1`
2	Cytosol	细胞质基质	0.80000	`XP_057808355.1`
3	Cytoplasmic granule	细胞质颗粒	0.40000	`XP_057808355.1`
4	Cytoplasmic ribonucleoprotein granule	Cytoplasmic ribonucleoprotein granule	0.20000	`XP_057808355.1`
5	Stress granule	Stress granule	0.20000	`XP_057808355.1`

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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
`Chr4:270566`	`G`	`A`	EMS_canonical_SNV	CDS_variant	5	B11,B126,C5,C74,D1
`Chr4:270606`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	A2
`Chr4:271128`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	D3
`Chr4:271141`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	A18,C49
`Chr4:271159`	`C`	`T`	EMS_canonical_SNV	CDS_variant	3	A19,C40,C62
`Chr4:271227`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B15
`Chr4:271239`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B4
`Chr4:271266`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B77
`Chr4:271756`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B5
`Chr4:272856`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B108
`Chr4:272861`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B24
`Chr4:272883`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	C21

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_057808355.1

358 aa

179

358

Stm1_N

HABP4_PAI-RBP1

PF09598 Stm1_N 1-69 aa PF04774 HABP4_PAI-RBP1 149-255 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057808355.1`	Pfam	`PF09598`	Stm1_N	Family	1	69	1.3e-20	74.6	Stm1
`XP_057808355.1`	Pfam	`PF04774`	HABP4_PAI-RBP1	Family	149	255	1.2e-25	91.1	Hyaluronan / mRNA binding family

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_057952372.1
AGATAAGATCAACGGATGAGATTACTTCTCTCTTCTTTCTTACATTTAGGCCATTTTCATATAAATAAAAACATTTACGTATATAACAGTCACCGCAGTGTGTTTAGATAAACCTCACTATACTCACTGTTGATTGCGGCTAGGGTTTGGCTCTCTCTTTATCTCTCTCCTCTTCAGTCTCTCACCTCTTCTTCCGGTCTTTCGAGACTCTTAGACCTGTTGATTCGAGACTCTTAGATCTGTTGATTCATACACTCAAT...

CDS

1 records

Download CDS FASTA

LOC131022838
ATGGCGACGCTAAACCCATTCGATTTGCTGGGCGACGATACGGAGGACCCCTCGCTGCTTGCAGCTCAGCAGCAGAAGATCGAGCCCAAAAAAAGCGTTGCACCACCGACCAAGCAGCCAGCGCAGCCGAAGCTCCCCTCCAAGCCGCTGCCCCCGGCTCAGGCTGTAAGAGAGGCAAAATTTGATTCTGCTCGAGGTGGACGTGGTCGAGGACGTGGATATGCTCGTGGTGCTGGTGTGGGCCCCAATAGAGACTTTGC...

Protein

1 records

Download Protein FASTA

XP_057808355.1
MATLNPFDLLGDDTEDPSLLAAQQQKIEPKKSVAPPTKQPAQPKLPSKPLPPAQAVREAKFDSARGGRGRGRGYARGAGVGPNRDFANNENSYGNKEVFAPQGAPDEVDGKPSERRGGGYGGPRGSFRGGRRGGFSNGDAGEGERDRIRRPLERRSGTGRGTEMKREGAGRGNWGMQTDELAQVTEEVVNEDDKNLNLEKPSGEEDAAENVEKEATKDENEEKPEDKEMTLEEYEKLLEEKRKALLALKSEERKVDAKEF...

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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