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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

SmilChr02G001784

Chromosome: Chr02 Coordinates: 32612339-32619547 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr02G001784
NameSmilChr02G001784
Descriptionsodium/calcium exchanger NCL2-like
Chromosome / SeqIDChr02 / NC_080388.1
Coordinates and Strand32612339 - 32619547 / +

ID Mapping

NCBI Gene IDLOC131012034
GeneID131012034
locus_tag-
NCBI NameLOC131012034
Original querySmilChr02G001784

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionsodium/calcium exchanger NCL2-like
Productsodium/calcium exchanger NCL2-like
ArabidopsisAT1G53210 (AT1G53210)
sodium/calcium exchanger family protein / calcium-binding EF hand family protein [Source:NCBI gene (formerly Entrezgene);Acc:841755]
identity=39.3; qcov=0.496; evalue=2.58e-81; confidence=medium
RiceOs01g0212400 (OsEFCAX1)
sodium/calcium exchanger NCL1-like [Source:NCBI gene (formerly Entrezgene);Acc:4325568]
identity=41.2; qcov=0.457; evalue=3.68e-77; confidence=medium
GOGO:0005509 (calcium ion binding); GO:0006874 (intracellular calcium ion homeostasis); GO:0015369 (calcium:proton antiporter activity); GO:0016020 (membrane); GO:0070588 (calcium ion transmembrane transport)
KEGG-
PfamPF01699 (Na_Ca_ex); PF13499 (EF-hand_7)
InterPro-
eggNOG-
NRGeneID:131012034

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cell membrane 细胞膜 1.00000 XP_057795924.1
2 Vacuole 液泡 0.60000 XP_057795924.1
3 Vacuole membrane 液泡膜 0.40000 XP_057795924.1
4 Nucleus 细胞核 0.00000 XP_057795924.1
5 Chromosome 染色体 0.00000 XP_057795924.1

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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
Chr2:32612561 C T EMS_canonical_SNV CDS_variant 1 D10
Chr2:32612581 A AT 1bp_insertion frameshift_variant 5 B110,B140,B51,C48,D4
Chr2:32612581 A AT 1bp_insertion CDS_variant 5 B110,B140,B51,C48,D4
Chr2:32612620 G A EMS_canonical_SNV CDS_variant 1 A3
Chr2:32612671 CTG C 2bp_deletion frameshift_variant 24 A10,A11,A13,B100,B131,B26,B42,B43,B47,B58,B65,B66,B69,B81,B89,C15,C31,C32,C4,C5,C68,C71,C84,D11
Chr2:32612782 G A EMS_canonical_SNV CDS_variant 5 B106,B63,B73,B83,D4
Chr2:32617246 C T EMS_canonical_SNV CDS_variant 2 B37,B84
Chr2:32617535 CT C 1bp_deletion frameshift_variant 6 A21,A25,B113,B28,B50,C18
Chr2:32617957 C T EMS_canonical_SNV CDS_variant 2 A18,C79
Chr2:32618042 C T EMS_canonical_SNV CDS_variant 4 B24,B40,C78,D5
Chr2:32618095 CA C 1bp_deletion frameshift_variant 1 B104
Chr2:32618095 CA C 1bp_deletion CDS_variant 1 B104

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_057795924.1
707 aa
N
1
354
707
EF-hand_7
EF-hand_7
Na_Ca_ex
C
PF13499 EF-hand_7 304-369 aa PF13499 EF-hand_7 441-505 aa PF01699 Na_Ca_ex 551-695 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057795924.1 Pfam PF13499 EF-hand_7 Domain 304 369 2.3e-22 79.8 EF-hand domain pair
XP_057795924.1 Pfam PF13499 EF-hand_7 Domain 441 505 2.3e-22 79.8 EF-hand domain pair
XP_057795924.1 Pfam PF01699 Na_Ca_ex Family 551 695 7.6e-09 36.4 Sodium/calcium exchanger protein

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_057939941.1
AAGAATAGTATTATTAATGAACGTATCAAGTTGCAAACAGTCAACTTTGATGAATAAAAGCAAGATGTGTTAGTATAACAAGTCATCGCTGCTGAAAGTCGGCATGACACCTGGTCAGACGACGAAACTTCCATGGCTGCTAAATATATACATGTCTCTCTCTCTCTTGAAATTTCTGATTATATTTAAATCCACTCAAAATCCCTCATTTACTAATCATGACAACTAGTCTTCCATATATCATTCTTCTCCCACTATTA...

CDS

1 records

Download CDS FASTA
LOC131012034
ATGACAACTAGTCTTCCATATATCATTCTTCTCCCACTATTAATCATATCGGCGGCCGGGGTCGGGGCAAGACCCCGGCCGCTGACGAGCACGTTGGTATCCGATGGATACCAGCTGTCGTCTTCGTCTTCGTCTTCTCCTCCGGTGATACGAATGAAAACGAGCGAAGAGGAAGAGACGATTTGCAGGCAATTGTATGGTTTCCTGCCTTGCTCGGAGAGCATGGGCGGGCATTTGTTCCTGATTTTGGTGTATGAATA...

Protein

1 records

Download Protein FASTA
XP_057795924.1
MTTSLPYIILLPLLIISAAGVGARPRPLTSTLVSDGYQLSSSSSSSPPVIRMKTSEEEETICRQLYGFLPCSESMGGHLFLILVYEYLLFHGESYVGWGGERIFKILGPGAFGASAFQLIGSLPEALILLGSGLWSNDETAQECMVTGIGLLAGSTILLLTLLWGTCVLLAAHTFRPDSLSHSHSRLQTFFFSLWPGYGVLTDSDTTYTARIMLLSVVPLAFVQVPGIFGFSSSAKRHFLLALLLVSIIFLLSYFFYQFF...

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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