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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

SmilChr01G000016

Chromosome: Chr01 Coordinates: 346189-354787 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr01G000016
NameSmilChr01G000016
Descriptiongamma-tubulin complex component 2-like
Chromosome / SeqIDChr01 / NC_080387.1
Coordinates and Strand346189 - 354787 / +

ID Mapping

NCBI Gene IDLOC131007163
GeneID131007163
locus_tag-
NCBI NameLOC131007163
Original queryLOC131007163

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptiongamma-tubulin complex component 2-like
Productgamma-tubulin complex component 2-like
ArabidopsisAT5G17410 (AT5G17410)
Spc97 / Spc98 family of spindle pole body (SBP) component [Source:NCBI gene (formerly Entrezgene);Acc:831607]
identity=72.5; qcov=0.995; evalue=0; confidence=high
RiceOs04g0501700
-
identity=70.3; qcov=1.01; evalue=0; confidence=high
GOGO:0000278 (mitotic cell cycle); GO:0000922 (spindle pole); GO:0000923 (equatorial microtubule organizing center); GO:0005813 (centrosome); GO:0007020 (microtubule nucleation); GO:0008275 (gamma-tubulin small complex); GO:0031122 (cytoplasmic microtubule organization); GO:0043015 (gamma-tubulin binding); GO:0051011 (microtubule minus-end binding); GO:0051225 (spindle assembly); GO:0051321 (meiotic cell cycle)
KEGG-
PfamPF04130 (GCP_C_terminal); PF17681 (GCP_N_terminal)
InterPro-
eggNOG-
NRGeneID:131007163

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cytoplasm 细胞质 1.00000 XP_057790306.1
2 Cytosol 细胞质基质 0.40000 XP_057790306.1
3 Golgi apparatus 高尔基体 0.20000 XP_057790306.1
4 Chromosome 染色体 0.20000 XP_057790308.1
5 Trans-golgi network Trans-golgi network 0.20000 XP_057790306.1

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
Chr1:351201 G A EMS_canonical_SNV CDS_variant 5 B117,B30,B82,C58,D2
Chr1:351367 C T EMS_canonical_SNV CDS_variant 2 B78,D4
Chr1:351382 G A EMS_canonical_SNV CDS_variant 2 C72,D2
Chr1:351736 G A EMS_canonical_SNV CDS_variant 2 B140,B42
Chr1:351743 AG A 1bp_deletion frameshift_variant 125 A10,A14,A15,A16,A18,A2,A25,A3,A4,A5,A8,B101,B105,B107,B108,B109,B110,B112,B113,B117,B119,B122,B123,B124,B126,B128,B129,B131,B136,B16,B19,B2,B20,B22,B24,B26,B3,B30,B32,B33,B34,B37,B38,B39,B40,B42,B45,B47,B50,B52,B54,B55,B64,B66,B69,B77,B78,B79,B8,B83,B84,B85,B86,B88,B89,B9,B92,B94,B99,C1,C14,C15,C16,C17,C19,C21,C22,C23,C24,C25,C28,C29,C31,C32,C33,C34,C36,C37,C38,C40,C41,C42,C44,C45,C48,C5,C52,C54,C55,C56,C57,C59,C6,C60,C63,C64,C65,C67,C69,C7,C72,C73,C77,C79,C80,C81,C82,C83,C87,D3,D4,D5,D6,D7,D9
Chr1:351748 A AC 1bp_insertion frameshift_variant 18 A14,A4,B10,B102,B2,B26,B36,B51,B89,C12,C29,C36,C47,C52,C57,C76,C8,D2
Chr1:351756 ACT A 2bp_deletion frameshift_variant 4 A3,A4,B7,C69
Chr1:351756 ACT A 2bp_deletion CDS_variant 4 A3,A4,B7,C69
Chr1:351763 G A EMS_canonical_SNV CDS_variant 3 A14,A4,B36
Chr1:354180 G A EMS_canonical_SNV CDS_variant 1 C46

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_057790306.1
693 aa
N
1
346
693
GCP_N_terminal
GCP_C_terminal
C
PF17681 GCP_N_terminal 60-351 aa PF04130 GCP_C_terminal 354-684 aa
XP_057790307.1
688 aa
N
1
344
688
GCP_N_terminal
GCP_C_terminal
C
PF17681 GCP_N_terminal 55-346 aa PF04130 GCP_C_terminal 349-679 aa
XP_057790308.1
640 aa
N
1
320
640
GCP_N_terminal
GCP_C_terminal
C
PF17681 GCP_N_terminal 7-298 aa PF04130 GCP_C_terminal 301-631 aa
XP_057790309.1
640 aa
N
1
320
640
GCP_N_terminal
GCP_C_terminal
C
PF17681 GCP_N_terminal 7-298 aa PF04130 GCP_C_terminal 301-631 aa
XP_057790310.1
599 aa
N
1
300
599
GCP_N_terminal
GCP_C_terminal
C
PF17681 GCP_N_terminal 2-257 aa PF04130 GCP_C_terminal 260-590 aa
XP_057790311.1
599 aa
N
1
300
599
GCP_N_terminal
GCP_C_terminal
C
PF17681 GCP_N_terminal 2-257 aa PF04130 GCP_C_terminal 260-590 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057790306.1 Pfam PF17681 GCP_N_terminal Domain 60 351 1.5e-77 261.8 Gamma tubulin complex component N-terminal
XP_057790306.1 Pfam PF04130 GCP_C_terminal Domain 354 684 2.8e-63 214.9 Gamma tubulin complex component C-terminal
XP_057790307.1 Pfam PF17681 GCP_N_terminal Domain 55 346 1.5e-77 261.8 Gamma tubulin complex component N-terminal
XP_057790307.1 Pfam PF04130 GCP_C_terminal Domain 349 679 2.8e-63 215.0 Gamma tubulin complex component C-terminal
XP_057790308.1 Pfam PF17681 GCP_N_terminal Domain 7 298 1.3e-77 262.0 Gamma tubulin complex component N-terminal
XP_057790308.1 Pfam PF04130 GCP_C_terminal Domain 301 631 2.3e-63 215.2 Gamma tubulin complex component C-terminal
XP_057790309.1 Pfam PF17681 GCP_N_terminal Domain 7 298 1.3e-77 262.0 Gamma tubulin complex component N-terminal
XP_057790309.1 Pfam PF04130 GCP_C_terminal Domain 301 631 2.3e-63 215.2 Gamma tubulin complex component C-terminal
XP_057790310.1 Pfam PF17681 GCP_N_terminal Domain 2 257 5.2e-71 240.3 Gamma tubulin complex component N-terminal
XP_057790310.1 Pfam PF04130 GCP_C_terminal Domain 260 590 9.6e-64 216.5 Gamma tubulin complex component C-terminal
XP_057790311.1 Pfam PF17681 GCP_N_terminal Domain 2 257 5.2e-71 240.3 Gamma tubulin complex component N-terminal
XP_057790311.1 Pfam PF04130 GCP_C_terminal Domain 260 590 9.6e-64 216.5 Gamma tubulin complex component 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

6 records

Download cDNA FASTA
XM_057934324.1
AATAAAATTTCCAAAATTTTGAATTGAAGAGACAAATCTCTTCTCTCGCCTCTCTTCGTCTCTCTCCTCTCACACTCTTGTCGCCCCCGCTTCCGTCCGGTCGCCTCCGCACTACCGCCACAGGCTGCAACCGCGCCTCCACCCTCAGTCGACGGCCCCTCCCCCGTCCGCAGCCCTCCGTTCGTCTCCGTCCTCAGCAGCAGTTTCCTGCTTTAAGCCCGCCAAGTGCCCTTCCTTCGTCAGTCAGCAGTTGATGGATG...
XM_057934323.1
CAAAATTTTGAATTGAAGAGACAAATCTCTTCTCTCGCCTCTCTTCGTCTCTCTCCTCTCACACTCTTGTCGCCCCCGCTTCCGTCCGGTCGCCTCCGCACTACCGCCACAGGCTGCAACCGCGCCTCCACCCTCAGTCGACGGCCCCTCCCCCGTCCGCAGCCCTCCGTTCGTCTCCGTCCTCAGCAGCAGTTTCCTGCTTTAAGCCCGCCAAGTGCCCTTCCTTCGTCAGTCAGCAGTTGATGGATGAATACCATAAG...

CDS

6 records

Download CDS FASTA
LOC131007163
ATGGATGAATACCATAAGCACATGCTGATCGAACCTTCGAAGCAGCCGTTGCGTGCACCAATTGAAGCTTCAAAGCAGCCATCTGTACTTGAAGGATGTAGATCTTCTGGGGTGGACAAACCCATAGGTTGCTTCCATGCTGCAATTCAGTTGTGTCTTATGCAGGAGTTAATTGTTATTGACGATCTCTTGTCAGCATTGGTTGGGATTGACGGACGTTATATCTCTATCCGTAGAGTACACGGGAAGGATGATACTGT...
LOC131007163
ATGGATGAATACCATAAGCACATGCTGATCGAACCTTCGAAGCAGCCGTTGCGTGCACCAATTGAAGCTTCAAAGCAGCCATCTGTACTTGAAGGATGTAGATCTTCTGGGGTGGACAAACCCATAGGTTGCTTCCATGCTGCAATTCAGGAGTTAATTGTTATTGACGATCTCTTGTCAGCATTGGTTGGGATTGACGGACGTTATATCTCTATCCGTAGAGTACACGGGAAGGATGATACTGTATCCTTTCAAGTTGA...

Protein

6 records

Download Protein FASTA
XP_057790306.1
MDEYHKHMLIEPSKQPLRAPIEASKQPSVLEGCRSSGVDKPIGCFHAAIQLCLMQELIVIDDLLSALVGIDGRYISIRRVHGKDDTVSFQVDASMDLALQESAKRIFPLCESYLLINQFVESRSQFKSGLVNHAFAAALRTLLLDYQAMVAQLEHQFRLGKLSVQGLWFYCQPMLGSMQALSIVIKKASASNFIGSAVLNLLQSQAKAMAGDHVVRSLLEKMSQSASQAYLGILERWVYEGVIDDPYGEFFIAENKSLQK...
XP_057790307.1
MDEYHKHMLIEPSKQPLRAPIEASKQPSVLEGCRSSGVDKPIGCFHAAIQELIVIDDLLSALVGIDGRYISIRRVHGKDDTVSFQVDASMDLALQESAKRIFPLCESYLLINQFVESRSQFKSGLVNHAFAAALRTLLLDYQAMVAQLEHQFRLGKLSVQGLWFYCQPMLGSMQALSIVIKKASASNFIGSAVLNLLQSQAKAMAGDHVVRSLLEKMSQSASQAYLGILERWVYEGVIDDPYGEFFIAENKSLQKESLMQ...

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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