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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

SmilChr02G002251

Chromosome: Chr02 Coordinates: 39936272-39942429 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr02G002251
NameSmilChr02G002251
Descriptionuncharacterized SmilChr02G002251
Chromosome / SeqIDChr02 / NC_080388.1
Coordinates and Strand39936272 - 39942429 / +

ID Mapping

NCBI Gene IDLOC131011183
GeneID131011183
locus_tag-
NCBI NameLOC131011183
Original querySmilChr02G002251

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptiontrafficking protein particle complex subunit-like protein [Source:NCBI gene (formerly Entrezgene);Acc:819408]; symbol=AT2G47960; hit=AT2G47960; species=arabidopsis; confidence=high
Producttrafficking protein particle complex subunit-like protein [Source:NCBI gene (formerly Entrezgene);Acc:819408]; symbol=AT2G47960; hit=AT2G47960; species=arabidopsis; confidence=high
ArabidopsisAT2G47960 (AT2G47960)
trafficking protein particle complex subunit-like protein [Source:NCBI gene (formerly Entrezgene);Acc:819408]
identity=65.6; qcov=0.967; evalue=0; confidence=high
RiceOs10g0498800
-
identity=46; qcov=0.14; evalue=7.51e-12; confidence=weak
GOGO:1990072 (TRAPPIII protein complex)
KEGG-
PfamPF06159 (TRAPPC13_N); PF23643 (TRAPPC13_C); PF23647 (TRAPPC13_M)
InterPro-
eggNOG-
NRGeneID:131011183

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cytoplasm 细胞质 0.60000 XP_057794965.1
2 Golgi apparatus 高尔基体 0.60000 XP_057794965.1
3 Cytoplasmic vesicle 细胞质囊泡 0.40000 XP_057794965.1
4 Autophagic vesicle Autophagic vesicle 0.20000 XP_057794965.1
5 Autophagosome Autophagosome 0.20000 XP_057794965.1

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
Chr2:39936569 G A EMS_canonical_SNV CDS_variant 2 B56,B96
Chr2:39936570 C T EMS_canonical_SNV CDS_variant 1 A24
Chr2:39936596 C T EMS_canonical_SNV CDS_variant 4 B32,B37,B6,C63
Chr2:39939263 C T EMS_canonical_SNV CDS_variant 2 A24,B139
Chr2:39939369 G A EMS_canonical_SNV CDS_variant 5 A1,A13,B117,C27,C83
Chr2:39939370 C T EMS_canonical_SNV CDS_variant 5 A1,A13,B117,C27,C83
Chr2:39940081 C T EMS_canonical_SNV CDS_variant 2 B80,C61
Chr2:39940082 G A EMS_canonical_SNV CDS_variant 3 A24,B104,B139
Chr2:39942142 TGA T 2bp_deletion CDS_variant 1 A24

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_057794965.1
451 aa
N
1
226
451
TRAPPC13_N
TRAPPC13_M
TRAPPC13_C
C
PF06159 TRAPPC13_N 18-205 aa PF23647 TRAPPC13_M 209-329 aa PF23643 TRAPPC13_C 348-439 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057794965.1 Pfam PF06159 TRAPPC13_N Domain 18 205 2.1e-36 126.2 Trafficking protein particle complex subunit 13, N-terminal
XP_057794965.1 Pfam PF23647 TRAPPC13_M Domain 209 329 1.5e-22 81.1 Trafficking protein particle complex subunit 13, middle domain
XP_057794965.1 Pfam PF23643 TRAPPC13_C Domain 348 439 3.5e-16 59.8 Trafficking protein particle complex subunit 13, C-terminal

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_057938982.1
GAAGCGCGCTTTCTAGTCAACAGTCTTCTCTGACCATTTCTACACTGCTTCCGACTGTCATCAATTCAAATCCCAGCAGCTCCGGCAACTCAACAAACAAAAAACCGATGAGTAGCGGCAGCGGCGGTGGCGGAGGCGGCGGAGGTCAACCGGCGACGCACTCATTGGCGTTTAGAGTGATGCGTCTCTGCCGCCCGACGCTCCACGTCGACAATTCCCCTCTCAAATTCGACCCCTGCGATCTCCTCTTCGGCGAGGAC...

CDS

1 records

Download CDS FASTA
LOC131011183
ATGAGTAGCGGCAGCGGCGGTGGCGGAGGCGGCGGAGGTCAACCGGCGACGCACTCATTGGCGTTTAGAGTGATGCGTCTCTGCCGCCCGACGCTCCACGTCGACAATTCCCCTCTCAAATTCGACCCCTGCGATCTCCTCTTCGGCGAGGACCTCTTCGACGATCCAATCGCGGCTTCGCACCTCCCTCGCCTCCTCGGCGGCCAATCGAACGCCGCGGCCTTAGATCCGGCCGACCTCAGCTACCGCGGCAGATTCCT...

Protein

1 records

Download Protein FASTA
XP_057794965.1
MSSGSGGGGGGGGQPATHSLAFRVMRLCRPTLHVDNSPLKFDPCDLLFGEDLFDDPIAASHLPRLLGGQSNAAALDPADLSYRGRFLLHQPTDSLGLPGLLVLPQSFGAIYLGETFCSYISINNSSNFEVRDVVIKAEIQTERQRLLLLDTSKSPVESIRAGGRYDFIVEHDVKELGAHTLVCTALYTDGDNERKYLPQFFKFMVSNPLSVRTKVRSVKDTTFLEACIENHTKSDLYMDQVEFEPAQYWSATVLKAANHA...

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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JBrowse

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