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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

SmilChr05G001061

Chromosome: Chr05 Coordinates: 8770560-8774801 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr05G001061
NameSmilChr05G001061
Descriptionuncharacterized SmilChr05G001061
Chromosome / SeqIDChr05 / NC_080391.1
Coordinates and Strand8770560 - 8774801 / +

ID Mapping

NCBI Gene IDLOC131025483
GeneID131025483
locus_tag-
NCBI NameLOC131025483
Original querySmilChr05G001061

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionhit=Os08g0202300; species=rice; confidence=weak
Producthit=Os08g0202300; species=rice; confidence=weak
ArabidopsisAT3G01410 (AT3G01410)
Polynucleotidyl transferase, ribonuclease H-like superfamily protein [Source:NCBI gene (formerly Entrezgene);Acc:821319]
identity=44.3; qcov=0.075; evalue=7.01e-13; confidence=weak
RiceOs08g0202300
-
identity=31.6; qcov=0.286; evalue=2.72e-58; confidence=weak
GOGO:0003676 (nucleic acid binding); GO:0004523 (RNA-DNA hybrid ribonuclease activity); GO:0015074 (DNA integration)
KEGG-
PfamPF00078 (RVT_1); PF13456 (RVT_3); PF17917 (RT_RNaseH); PF17919 (RT_RNaseH_2); PF17921 (Integrase_H2C2); PF31073 (DUF8803)
InterPro-
eggNOG-
NRGeneID:131025483

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cytoplasm 细胞质 1.00000 XP_057811261.1
2 Cytosol 细胞质基质 0.80000 XP_057811261.1
3 Nucleus 细胞核 0.20000 XP_057811261.1
4 Chromosome 染色体 0.00000 XP_057811261.1
5 Centromere 着丝粒 0.00000 XP_057811261.1

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
Chr5:8770580 G A EMS_canonical_SNV CDS_variant 1 A19
Chr5:8770625 C T EMS_canonical_SNV CDS_variant 1 A19
Chr5:8770629 AC A 1bp_deletion frameshift_variant 1 A19
Chr5:8770629 AC A 1bp_deletion CDS_variant 1 A19
Chr5:8770697 C T EMS_canonical_SNV CDS_variant 4 B10,B103,B79,C16
Chr5:8770712 TC T 1bp_deletion frameshift_variant 1 B74
Chr5:8770712 TC T 1bp_deletion CDS_variant 1 B74
Chr5:8770751 G A EMS_canonical_SNV CDS_variant 1 B104
Chr5:8770753 G A EMS_canonical_SNV CDS_variant 5 A3,B104,B139,C49,C78
Chr5:8770768 C T EMS_canonical_SNV CDS_variant 5 B10,B50,B52,B79,C16
Chr5:8770779 C T EMS_canonical_SNV CDS_variant 1 B35
Chr5:8770797 G A EMS_canonical_SNV CDS_variant 1 B69

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_057811261.1
1292 aa
N
1
646
1292
RVT_1
RT_RNaseH_2
RT_RNaseH
RVT_3
Integrase_H2C2
DUF8803
C
PF00078 RVT_1 408-567 aa PF17919 RT_RNaseH_2 631-729 aa PF17917 RT_RNaseH 660-757 aa PF13456 RVT_3 809-927 aa PF17921 Integrase_H2C2 1003-1054 aa PF31073 DUF8803 1227-1290 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057811261.1 Pfam PF00078 RVT_1 Domain 408 567 2.3e-33 116.5 Reverse transcriptase (RNA-dependent DNA polymerase)
XP_057811261.1 Pfam PF17919 RT_RNaseH_2 Domain 631 729 4.6e-23 81.9 RNase H-like domain found in reverse transcriptase
XP_057811261.1 Pfam PF17917 RT_RNaseH Domain 660 757 7.4e-18 65.3 RNase H-like domain found in reverse transcriptase
XP_057811261.1 Pfam PF13456 RVT_3 Domain 809 927 1e-18 68.1 Reverse transcriptase-like
XP_057811261.1 Pfam PF17921 Integrase_H2C2 Domain 1003 1054 4.9e-10 40.1 Integrase zinc binding domain
XP_057811261.1 Pfam PF31073 DUF8803 Domain 1227 1290 4.5e-27 94.4 Domain of unknown function (DUF8803)

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_057955278.1
ATGAGGGCACCAGCCGACCAGAGAGATAGATCTAAGTGGTGCGAATTTCATGCCGACCATGGACACCGAACGGAGGATTGCATTGCATTACGATTGGAAGTGGCGCATTTACTCAAAGAAGGTCACCTAACTGAGTTCCTAACAGACAAGGGTCAACACACCCTCAAGCATGGAAATGATAGACGAGACGAGCGCAGAGAAGTCACCCCACCCAACCCGCCAAACCATGAGAGAACAGTCAATGTCATTTCTGGCGGATC...

CDS

1 records

Download CDS FASTA
LOC131025483
ATGAGGGCACCAGCCGACCAGAGAGATAGATCTAAGTGGTGCGAATTTCATGCCGACCATGGACACCGAACGGAGGATTGCATTGCATTACGATTGGAAGTGGCGCATTTACTCAAAGAAGGTCACCTAACTGAGTTCCTAACAGACAAGGGTCAACACACCCTCAAGCATGGAAATGATAGACGAGACGAGCGCAGAGAAGTCACCCCACCCAACCCGCCAAACCATGAGAGAACAGTCAATGTCATTTCTGGCGGATC...

Protein

1 records

Download Protein FASTA
XP_057811261.1
MRAPADQRDRSKWCEFHADHGHRTEDCIALRLEVAHLLKEGHLTEFLTDKGQHTLKHGNDRRDERREVTPPNPPNHERTVNVISGGSEVSGITHSAAKRHTRQARSSRTRESVTGQAMTDQPTQTISFQTTESDKLLNPHHDALVISIYIANCLTKRVLIDNGSSANIMFINAFREMGLNESNITRKTAVLIGFSGESKTIVGEIDLSIYAEWVNLSTRFLVIDAPSAFNVILGRPWIHDMEAVPSTFHQVEEGSSYTKT...

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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