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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

SmilChr05G002461

Chromosome: Chr05 Coordinates: 27128200-27132674 Strand: - Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr05G002461
NameSmilChr05G002461
Descriptionprotein PLASTID TRANSCRIPTIONALLY ACTIVE 14
Chromosome / SeqIDChr05 / NC_080391.1
Coordinates and Strand27128200 - 27132674 / -

ID Mapping

NCBI Gene IDLOC131026235
GeneID131026235
locus_tag-
NCBI NameLOC131026235
Original queryLOC131026235

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Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionprotein PLASTID TRANSCRIPTIONALLY ACTIVE 14
Productprotein PLASTID TRANSCRIPTIONALLY ACTIVE 14
ArabidopsisAT4G20130 (PTAC14)
plastid transcriptionally active 14 [Source:NCBI gene (formerly Entrezgene);Acc:827759]
identity=73.2; qcov=0.91; evalue=0; confidence=high
RiceOs05g0587200 (OsSET23)
-
identity=75.8; qcov=0.198; evalue=3.83e-47; confidence=weak
GOGO:0000427 (plastid-encoded plastid RNA polymerase complex); GO:0005515 (protein binding); GO:0009534 (chloroplast thylakoid); GO:0009658 (chloroplast organization); GO:0010027 (thylakoid membrane organization); GO:0016279 (protein-lysine N-methyltransferase activity); GO:0018026 (peptidyl-lysine monomethylation); GO:0042793 (plastid transcription)
KEGG-
PfamPF00856 (SET); PF09273 (Rubis-subs-bind)
InterPro-
eggNOG-
NRGeneID:131026235

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Chloroplast 叶绿体 1.00000 XP_057812006.1
2 Chloroplast stroma 叶绿体基质 1.00000 XP_057812006.1
3 Chloroplast thylakoid 类囊体 0.20000 XP_057812006.1
4 Nucleus 细胞核 0.00000 XP_057812006.1
5 Chromosome 染色体 0.00000 XP_057812006.1

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
Chr5:27128885 C T EMS_canonical_SNV CDS_variant 1 B37
Chr5:27129170 G A EMS_canonical_SNV CDS_variant 4 B56,B96,C52,C84
Chr5:27129219 C T EMS_canonical_SNV CDS_variant 5 A2,B21,B40,B75,B77
Chr5:27130358 C T EMS_canonical_SNV CDS_variant 2 C52,C84
Chr5:27131497 G A EMS_canonical_SNV CDS_variant 5 B39,B74,B77,B79,D7
Chr5:27132041 C T EMS_canonical_SNV CDS_variant 1 C3
Chr5:27132350 G A EMS_canonical_SNV CDS_variant 1 D10
Chr5:27132465 G A EMS_canonical_SNV CDS_variant 5 B130,B136,B58,C33,C82
Chr5:27132467 G A EMS_canonical_SNV CDS_variant 1 C8

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_057812006.1
480 aa
N
1
240
480
SET
Rubis-subs-bind
C
PF00856 SET 97-320 aa PF09273 Rubis-subs-bind 407-461 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057812006.1 Pfam PF00856 SET Family 97 320 4.5e-10 40.6 SET domain
XP_057812006.1 Pfam PF09273 Rubis-subs-bind Domain 407 461 2.7e-07 32.0 Rubisco LSMT substrate-binding

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_057956023.1
ATTGGCTTATGGTTTATCATAACATGCCTACCAAACATAGGTAAAGTGAGAAAAAAAAGAAGTAAAAAAGGATAAACCCAATGGAGGTTTTGCAGAACGCCCGACAACGGAAGCGGCTGTAGATGGATAACGTTTCGGTTTGCTGAAATTTCCGCCAAAACGGGTACACTGCAACACAAGCAATGGCTATGTCGCTCCTGCATTCACCACCGTACTGCCTCTTCACCCACCACCGCCGCCGCGGCCAGCAGGTAACTCCG...

CDS

1 records

Download CDS FASTA
LOC131026235
ATGGCTATGTCGCTCCTGCATTCACCACCGTACTGCCTCTTCACCCACCACCGCCGCCGCGGCCAGCAGGTAACTCCGCGAAGTGCTTCTGTGCTGCGTGCGGCTATGATTACTAATGAAGACACATCTTCTGCAATTTCCACGTCCGATTTCCCACTCTTCCAAACCACCCTCATTCCCCAACCTACTGCTGCTTCTCAGTTGGAGCCAGCGGATCCTGATTTCTATAAGATAGGATATGTTAGGAATATGCGAGCTTA...

Protein

1 records

Download Protein FASTA
XP_057812006.1
MAMSLLHSPPYCLFTHHRRRGQQVTPRSASVLRAAMITNEDTSSAISTSDFPLFQTTLIPQPTAASQLEPADPDFYKIGYVRNMRAYGIEFREGPDGFGVYASKDIEPLRRARLIMEIPLELMLTISQKLPWMFFPDIIPVGHPIFDIINSTNPETDWDLRMACLLLYAFDCKDNFWQLYGDFLPATDECTSFLLATEEDLLELQDTELASTIRQQQQRALEFWDKNWHSAVPLKIKRLALEPERFLWAMSMAQSRCINK...

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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