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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.
Examples

Resolved gene

SmilChr03G002700

Chromosome: Chr03 Coordinates: 42965603-42969421 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr03G002700
NameSmilChr03G002700
Descriptionuncharacterized SmilChr03G002700
Chromosome / SeqIDChr03 / NC_080389.1
Coordinates and Strand42965603 - 42969421 / +

ID Mapping

NCBI Gene IDLOC131018835
GeneID131018835
locus_tag-
NCBI NameLOC131018835
Original querySmilChr03G002700

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Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionhit=Os06g0484800; species=rice; confidence=low
Producthit=Os06g0484800; species=rice; confidence=low
ArabidopsisAT4G29090 (AT4G29090)
Ribonuclease H-like superfamily protein [Source:NCBI gene (formerly Entrezgene);Acc:829030]
identity=27; qcov=0.492; evalue=1.41e-52; confidence=low
RiceOs06g0484800
-
identity=28.7; qcov=0.708; evalue=3.91e-101; confidence=low
GOGO:0003676 (nucleic acid binding); GO:0004523 (RNA-DNA hybrid ribonuclease activity)
KEGG-
PfamPF00078 (RVT_1); PF03372 (Exo_endo_phos); PF13456 (RVT_3); PF13966 (zf-RVT)
InterPro-
eggNOG-
NRGeneID:131018835

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cytoplasm 细胞质 1.00000 XP_057803521.1
2 Cytosol 细胞质基质 1.00000 XP_057803521.1
3 Nucleus 细胞核 0.40000 XP_057803521.1
4 Chromosome 染色体 0.00000 XP_057803521.1
5 Centromere 着丝粒 0.00000 XP_057803521.1

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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
Chr3:42965611 C CCA 2bp_insertion frameshift_variant 6 B135,B3,B45,B49,C58,C87
Chr3:42965634 G A EMS_canonical_SNV CDS_variant 5 B32,B63,B64,C28,C34
Chr3:42965651 G A EMS_canonical_SNV CDS_variant 1 B108
Chr3:42965685 G A EMS_canonical_SNV stop_gained 3 B63,C34,C74
Chr3:42965685 G A EMS_canonical_SNV CDS_variant 3 B63,C34,C74
Chr3:42965700 G A EMS_canonical_SNV CDS_variant 1 C23
Chr3:42965723 C T EMS_canonical_SNV CDS_variant 1 B82
Chr3:42965724 C T EMS_canonical_SNV CDS_variant 1 C68
Chr3:42965725 G A EMS_canonical_SNV CDS_variant 3 B108,B22,B36
Chr3:42965729 G A EMS_canonical_SNV CDS_variant 3 B108,B22,B36
Chr3:42965756 C T EMS_canonical_SNV CDS_variant 2 B108,B22
Chr3:42965768 G A EMS_canonical_SNV CDS_variant 1 B3

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_057803521.1
1138 aa
N
1
569
1138
Exo_endo_phos
RVT_1
zf-RVT
RVT_3
C
PF03372 Exo_endo_phos 11-93 aa PF00078 RVT_1 364-529 aa PF13966 zf-RVT 812-880 aa PF13456 RVT_3 990-1111 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057803521.1 Pfam PF03372 Exo_endo_phos Domain 11 93 7.5e-06 26.6 Endonuclease/Exonuclease/phosphatase family
XP_057803521.1 Pfam PF00078 RVT_1 Domain 364 529 2.7e-21 77.1 Reverse transcriptase (RNA-dependent DNA polymerase)
XP_057803521.1 Pfam PF13966 zf-RVT Domain 812 880 1.1e-18 68.4 zinc-binding in reverse transcriptase
XP_057803521.1 Pfam PF13456 RVT_3 Domain 990 1111 7e-12 46.1 Reverse transcriptase-like

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_057947538.1
ATGATCATCACTGATACTAAAGGTGATTGGCGTTTCACCGGTTTTTACGGCTTCCCTGAAAGAGGTCGTCGACGTGAGTCCTGGAATCTCTTGCGGCGCCTGGCCGTCATCAACTCCTTACCGTGGGTTATTGCAGGAGATTTCAATGACCTCCTTGATCCCGGGGATAAAAGGGGTCGTGTGGATCACCCAAACTGGCTCTTCTCTGGCTTCAGATCTGCTATCATGGATTGCGGTCTCTCGGATATCCCTCTTACGGG...

CDS

1 records

Download CDS FASTA
LOC131018835
ATGATCATCACTGATACTAAAGGTGATTGGCGTTTCACCGGTTTTTACGGCTTCCCTGAAAGAGGTCGTCGACGTGAGTCCTGGAATCTCTTGCGGCGCCTGGCCGTCATCAACTCCTTACCGTGGGTTATTGCAGGAGATTTCAATGACCTCCTTGATCCCGGGGATAAAAGGGGTCGTGTGGATCACCCAAACTGGCTCTTCTCTGGCTTCAGATCTGCTATCATGGATTGCGGTCTCTCGGATATCCCTCTTACGGG...

Protein

1 records

Download Protein FASTA
XP_057803521.1
MIITDTKGDWRFTGFYGFPERGRRRESWNLLRRLAVINSLPWVIAGDFNDLLDPGDKRGRVDHPNWLFSGFRSAIMDCGLSDIPLTGHQYTWSRGLGTAHSVEERLDPGMATSAWKLLYPDAILMPLSVPISDHAPLLLRCKEKLTVVSESISIWAAHLTRHDRLAKSRLQIQIANIQGHTDLQSIKKLKHARQALANILLKEETHWRQRAKQHWLQEGDCNTKFFHTMASARRKKNSIVRLQRDDGSWTENVDDIKLVA...

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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