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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

SmilChr04G002119

Chromosome: Chr04 Coordinates: 34177739-34181453 Strand: - Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr04G002119
NameSmilChr04G002119
Description5-formyltetrahydrofolate cyclo-ligase, mitochondrial-like
Chromosome / SeqIDChr04 / NC_080390.1
Coordinates and Strand34177739 - 34181453 / -

ID Mapping

NCBI Gene IDLOC131021279
GeneID131021279
locus_tag-
NCBI NameLOC131021279
Original querySmilChr04G002119

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; KEGG smil; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description5-formyltetrahydrofolate cyclo-ligase, mitochondrial-like
Product5-formyltetrahydrofolate cyclo-ligase%2C mitochondrial-like
ArabidopsisAT5G13050 (5-FCL)
5-formyltetrahydrofolate cycloligase [Source:NCBI gene (formerly Entrezgene);Acc:831144]
identity=65.7; qcov=0.9; evalue=2.71e-106; confidence=high
RiceOs07g0578600
-
identity=63.8; qcov=0.851; evalue=6.22e-96; confidence=high
GOGO:0005739 (mitochondrion); GO:0009396 (folic acid-containing compound biosynthetic process); GO:0030272 (5-formyltetrahydrofolate cyclo-ligase activity); GO:0035999 (tetrahydrofolate interconversion)
KEGGsmil00670 (One carbon pool by folate - Salvia miltiorrhiza (redroot sage)); smil01100 (Metabolic pathways - Salvia miltiorrhiza (redroot sage)); smil04981 (Folate transport and metabolism - Salvia miltiorrhiza (redroot sage))
PfamPF01812 (5-FTHF_cyc-lig)
InterPro-
eggNOG-
NRGeneID:131021279

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Mitochondrion 线粒体 1.00000 XP_057806380.1
2 Chloroplast 叶绿体 0.80000 XP_057806380.1
3 Mitochondrion matrix 线粒体基质 0.20000 XP_057806380.1
4 Nucleus 细胞核 0.00000 XP_057806382.1
5 Chromosome 染色体 0.00000 XP_057806382.1

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
Chr4:34177962 TG T 1bp_deletion frameshift_variant 1 C6
Chr4:34177962 TG T 1bp_deletion CDS_variant 1 C6
Chr4:34178248 G A EMS_canonical_SNV CDS_variant 2 B110,B5
Chr4:34179219 C T EMS_canonical_SNV CDS_variant 2 B78,D4
Chr4:34179681 C T EMS_canonical_SNV CDS_variant 1 A22
Chr4:34179693 C T EMS_canonical_SNV CDS_variant 1 B41

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_057806380.1
283 aa
N
1
142
283
5-FTHF_cyc-lig
C
PF01812 5-FTHF_cyc-lig 59-266 aa
XP_057806381.1
283 aa
N
1
142
283
5-FTHF_cyc-lig
C
PF01812 5-FTHF_cyc-lig 59-266 aa
XP_057806382.1
269 aa
N
1
134
269
5-FTHF_cyc-lig
C
PF01812 5-FTHF_cyc-lig 45-252 aa
XP_057806383.1
269 aa
N
1
134
269
5-FTHF_cyc-lig
C
PF01812 5-FTHF_cyc-lig 45-252 aa
XP_057806384.1
269 aa
N
1
134
269
5-FTHF_cyc-lig
C
PF01812 5-FTHF_cyc-lig 45-252 aa
XP_057806386.1
269 aa
N
1
134
269
5-FTHF_cyc-lig
C
PF01812 5-FTHF_cyc-lig 45-252 aa
XP_057806387.1
269 aa
N
1
134
269
5-FTHF_cyc-lig
C
PF01812 5-FTHF_cyc-lig 45-252 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057806380.1 Pfam PF01812 5-FTHF_cyc-lig Domain 59 266 7.7e-30 104.9 5-formyltetrahydrofolate cyclo-ligase family
XP_057806381.1 Pfam PF01812 5-FTHF_cyc-lig Domain 59 266 7.7e-30 104.9 5-formyltetrahydrofolate cyclo-ligase family
XP_057806382.1 Pfam PF01812 5-FTHF_cyc-lig Domain 45 252 6.6e-30 105.1 5-formyltetrahydrofolate cyclo-ligase family
XP_057806383.1 Pfam PF01812 5-FTHF_cyc-lig Domain 45 252 6.6e-30 105.1 5-formyltetrahydrofolate cyclo-ligase family
XP_057806384.1 Pfam PF01812 5-FTHF_cyc-lig Domain 45 252 6.6e-30 105.1 5-formyltetrahydrofolate cyclo-ligase family
XP_057806386.1 Pfam PF01812 5-FTHF_cyc-lig Domain 45 252 6.6e-30 105.1 5-formyltetrahydrofolate cyclo-ligase family
XP_057806387.1 Pfam PF01812 5-FTHF_cyc-lig Domain 45 252 6.6e-30 105.1 5-formyltetrahydrofolate cyclo-ligase family

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

7 records

Download cDNA FASTA
XM_057950399.1
GTTTCAGAGAAAAGTCCTCGAATTGGGCCAATTACTAAATAAAAGCTTAGGCCTACTGCACGAAATGAATACTCGCGCCAGCCGCCGCCTTCTTCCGACGCAGCGTCGGTGACGCTTCCCCCGGCTCGCGTCAGCTCCACCCCGCTTCATTAAAGGTTTAATTAAAACAGCCCGCCGAGCGCCCCCCCCCCCCCCCCCCCCCCCCCAACACCGGTCAGACGATTCGGAATCTCAGATCAGGATAAGATTTGCAGAGCGGA...
XM_057950400.1
GTTTCAGAGAAAAGTCCTCGAATTGGGCCAATTACTAAATAAAAGCTTAGGCCTACTGCACGAAATGAATACTCGCGCCAGCCGCCGCCTTCTTCCGACGCAGCGTCGGTGACGCTTCCCCCGGCTCGCGTCAGCTCCACCCCGCTTCATTAAAGGTTTAATTAAAACAGCCCGCCGAGCGCCCCCCCCCCCCCCCCCCCCCCCCCAACACCGGTCAGACGATTCGGAATCTCAGATCAGGATAAGGTCGCCGCCTACAA...

CDS

7 records

Download CDS FASTA
LOC131021279
ATGACGATAATAGGTCGCCGCCTACAAAGATTTGCAGAGCGGATGATACTGCAGCTCGCTTTACCAACCGCCGCAACGCCTGCTTTACCCACCACCTTATCCGGTCTGAATTTACGCTCCTCCGCTACCATGAGCGCCGGGGGTATCGCCGCCGCACCTCTAGACGCCGTTTTCAAGGAGAAAAAGGCGCTTCGCTCCAGAGTGAGAAAGGAACTCAAGTCAATGGACCCCGCGCTCAGATCTCAAGAAGATGATGCAAT...
LOC131021279
ATGACGATAATAGGTCGCCGCCTACAAAGATTTGCAGAGCGGATGATACTGCAGCTCGCTTTACCAACCGCCGCAACGCCTGCTTTACCCACCACCTTATCCGGTCTGAATTTACGCTCCTCCGCTACCATGAGCGCCGGGGGTATCGCCGCCGCACCTCTAGACGCCGTTTTCAAGGAGAAAAAGGCGCTTCGCTCCAGAGTGAGAAAGGAACTCAAGTCAATGGACCCCGCGCTCAGATCTCAAGAAGATGATGCAAT...

Protein

7 records

Download Protein FASTA
XP_057806380.1
MTIIGRRLQRFAERMILQLALPTAATPALPTTLSGLNLRSSATMSAGGIAAAPLDAVFKEKKALRSRVRKELKSMDPALRSQEDDAIQRVVLEAPWFKSCTRLCAYISCAALREVDTSKVLSEILKNTAQDDHSQVRKKLYVPRVEDKNSFMRMLNITRMDDLIANSMDILEPQPCDAEGNEREDVMLADEPVDLFLLPGLAFDRSGRRIGRGGGYYDTFLTKYQELAKDRKWKKPLFVALSYSLQVLEDGVIPITPNDV...
XP_057806381.1
MTIIGRRLQRFAERMILQLALPTAATPALPTTLSGLNLRSSATMSAGGIAAAPLDAVFKEKKALRSRVRKELKSMDPALRSQEDDAIQRVVLEAPWFKSCTRLCAYISCAALREVDTSKVLSEILKNTAQDDHSQVRKKLYVPRVEDKNSFMRMLNITRMDDLIANSMDILEPQPCDAEGNEREDVMLADEPVDLFLLPGLAFDRSGRRIGRGGGYYDTFLTKYQELAKDRKWKKPLFVALSYSLQVLEDGVIPITPNDV...

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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