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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

SmilChr04G001585

Chromosome: Chr04 Coordinates: 26342507-26355706 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr04G001585
NameSmilChr04G001585
Descriptionclathrin heavy chain 1-like
Chromosome / SeqIDChr04 / NC_080390.1
Coordinates and Strand26342507 - 26355706 / +

ID Mapping

NCBI Gene IDLOC131020018
GeneID131020018
locus_tag-
NCBI NameLOC131020018
Original querySmilChr04G001585

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; KEGG smil; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionclathrin heavy chain 1-like
Productclathrin heavy chain 1-like
ArabidopsisAT3G11130 (AT3G11130)
Clathrin, heavy chain [Source:NCBI gene (formerly Entrezgene);Acc:820284]
identity=92.7; qcov=0.971; evalue=0; confidence=high
RiceOs11g0104900
-
identity=92; qcov=0.971; evalue=0; confidence=high
GOGO:0005198 (structural molecule activity); GO:0005794 (Golgi apparatus); GO:0005886 (plasma membrane); GO:0006886 (intracellular protein transport); GO:0006898 (receptor-mediated endocytosis); GO:0009506 (plasmodesma); GO:0009507 (chloroplast); GO:0030130 (clathrin coat of trans-Golgi network vesicle); GO:0030132 (clathrin coat of coated pit); GO:0032051 (clathrin light chain binding); GO:0071439 (clathrin complex)
KEGGsmil04142 (Lysosome biogenesis - Salvia miltiorrhiza (redroot sage)); smil04144 (Endocytosis - Salvia miltiorrhiza (redroot sage)); smil05100 (Bacterial invasion of epithelial cells - Salvia miltiorrhiza (redroot sage))
PfamPF00637 (Clathrin); PF01394 (Clathrin_propel); PF09268 (Clathrin-link); PF13838 (Clathrin_H_link)
InterPro-
eggNOG-
NRGeneID:131020018

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cytoplasm 细胞质 0.80000 XP_057804631.1
2 Cytosol 细胞质基质 0.80000 XP_057804631.1
3 Cytoplasmic vesicle 细胞质囊泡 0.60000 XP_057804631.1
4 Endocytic vesicle Endocytic vesicle 0.60000 XP_057804631.1
5 Clathrin-coated vesicle Clathrin-coated vesicle 0.60000 XP_057804631.1

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
Chr4:26344326 G A EMS_canonical_SNV CDS_variant 1 B64
Chr4:26344434 G A EMS_canonical_SNV CDS_variant 1 D7
Chr4:26344467 G A EMS_canonical_SNV CDS_variant 1 C64
Chr4:26344546 C T EMS_canonical_SNV CDS_variant 1 B131
Chr4:26346422 C T EMS_canonical_SNV CDS_variant 1 B95
Chr4:26346563 G A EMS_canonical_SNV CDS_variant 1 D11
Chr4:26346577 G A EMS_canonical_SNV CDS_variant 4 B123,B14,B44,C67
Chr4:26346625 G A EMS_canonical_SNV CDS_variant 4 A13,B104,B25,C13
Chr4:26346848 C T EMS_canonical_SNV CDS_variant 1 B33
Chr4:26346865 C T EMS_canonical_SNV CDS_variant 1 D3
Chr4:26346992 G A EMS_canonical_SNV CDS_variant 2 B42,B43
Chr4:26347321 C T EMS_canonical_SNV CDS_variant 2 B91,D10

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_057804631.1
1731 aa
N
1
866
1731
Clathrin_propel
Clathrin_propel
Clathrin-link
Clathrin_H_link
Clathrin
Clathrin
Clathrin
Clathrin
Clathrin
Clathrin
Clathrin
C
PF01394 Clathrin_propel 20-55 aa PF01394 Clathrin_propel 155-197 aa PF09268 Clathrin-link 344-367 aa PF13838 Clathrin_H_link 369-434 aa PF00637 Clathrin 557-659 aa PF00637 Clathrin 726-866 aa PF00637 Clathrin 875-1006 aa PF00637 Clathrin 1018-1156 aa PF00637 Clathrin 1169-1306 aa PF00637 Clathrin 1313-1457 aa PF00637 Clathrin 1463-1604 aa
XP_057804632.1
1706 aa
N
1
853
1706
Clathrin_propel
Clathrin_propel
Clathrin-link
Clathrin_H_link
Clathrin
Clathrin
Clathrin
Clathrin
Clathrin
Clathrin
Clathrin
C
PF01394 Clathrin_propel 20-55 aa PF01394 Clathrin_propel 155-197 aa PF09268 Clathrin-link 344-367 aa PF13838 Clathrin_H_link 369-434 aa PF00637 Clathrin 557-692 aa PF00637 Clathrin 701-841 aa PF00637 Clathrin 850-981 aa PF00637 Clathrin 993-1131 aa PF00637 Clathrin 1144-1281 aa PF00637 Clathrin 1288-1432 aa PF00637 Clathrin 1438-1579 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057804631.1 Pfam PF01394 Clathrin_propel Repeat 20 55 1.7e-33 113.8 Clathrin propeller repeat
XP_057804631.1 Pfam PF01394 Clathrin_propel Repeat 155 197 1.7e-33 113.8 Clathrin propeller repeat
XP_057804631.1 Pfam PF09268 Clathrin-link Repeat 344 367 7.6e-09 35.5 Clathrin, heavy-chain linker
XP_057804631.1 Pfam PF13838 Clathrin_H_link Repeat 369 434 9.5e-29 99.9 Clathrin-H-link
XP_057804631.1 Pfam PF00637 Clathrin Repeat 557 659 1.9e-212 696.3 Region in Clathrin and VPS
XP_057804631.1 Pfam PF00637 Clathrin Repeat 726 866 1.9e-212 696.3 Region in Clathrin and VPS
XP_057804631.1 Pfam PF00637 Clathrin Repeat 875 1006 1.9e-212 696.3 Region in Clathrin and VPS
XP_057804631.1 Pfam PF00637 Clathrin Repeat 1018 1156 1.9e-212 696.3 Region in Clathrin and VPS
XP_057804631.1 Pfam PF00637 Clathrin Repeat 1169 1306 1.9e-212 696.3 Region in Clathrin and VPS
XP_057804631.1 Pfam PF00637 Clathrin Repeat 1313 1457 1.9e-212 696.3 Region in Clathrin and VPS
XP_057804631.1 Pfam PF00637 Clathrin Repeat 1463 1604 1.9e-212 696.3 Region in Clathrin and VPS
XP_057804632.1 Pfam PF01394 Clathrin_propel Repeat 20 55 1.6e-33 113.9 Clathrin propeller repeat
XP_057804632.1 Pfam PF01394 Clathrin_propel Repeat 155 197 1.6e-33 113.9 Clathrin propeller repeat
XP_057804632.1 Pfam PF09268 Clathrin-link Repeat 344 367 7.4e-09 35.5 Clathrin, heavy-chain linker
XP_057804632.1 Pfam PF13838 Clathrin_H_link Repeat 369 434 9e-29 100.0 Clathrin-H-link
XP_057804632.1 Pfam PF00637 Clathrin Repeat 557 692 1.6e-215 706.3 Region in Clathrin and VPS
XP_057804632.1 Pfam PF00637 Clathrin Repeat 701 841 1.6e-215 706.3 Region in Clathrin and VPS
XP_057804632.1 Pfam PF00637 Clathrin Repeat 850 981 1.6e-215 706.3 Region in Clathrin and VPS
XP_057804632.1 Pfam PF00637 Clathrin Repeat 993 1131 1.6e-215 706.3 Region in Clathrin and VPS
XP_057804632.1 Pfam PF00637 Clathrin Repeat 1144 1281 1.6e-215 706.3 Region in Clathrin and VPS
XP_057804632.1 Pfam PF00637 Clathrin Repeat 1288 1432 1.6e-215 706.3 Region in Clathrin and VPS
XP_057804632.1 Pfam PF00637 Clathrin Repeat 1438 1579 1.6e-215 706.3 Region in Clathrin and VPS

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

2 records

Download cDNA FASTA
XM_057948648.1
TTTAGATCTCCCTCCCTCACTATTTTTCATTTTCCGACTCAGCAAAATTCCATTTTCGCTGTCGCATTTGCGTCTATATATAATACTGTACACTTCTTTACTTAGTTTCTTCTGCCTTTAGAAGAACCCCCCCTCTCTCTCTCTCTAGATCTTCTGTTTCTCTTCGGTTAGAGGGTACGAGGGTTTCTCCTTGCTTTCCAGATCTCGAGAACATCTGTGATACGCCGTCGTCCTTGGCTTAGATCCGCAGCTTCGATCTC...
XM_057948649.1
TTAGATCTCCCTCCCTCACTATTTTTCATTTTCCGACTCAGCAAAATTCCATTTTCGCTGTCGCATTTGCGTCTATATATAATACTGTACACTTCTTTACTTAGTTTCTTCTGCCTTTAGAAGAACCCCCCCTCTCTCTCTCTCTAGATCTTCTGTTTCTCTTCGGTTAGAGGGTACGAGGGTTTCTCCTTGCTTTCCAGATCTCGAGAACATCTGTGATACGCCGTCGTCCTTGGCTTAGATCCGCAGCTTCGATCTCG...

CDS

2 records

Download CDS FASTA
LOC131020018
ATGGCGGCTGCCAATGCTCCGATCACCATGAAAGAAGCGCTTACGTTGACTAGCTTAGGGATCAATCCCCAGTTCATTACTTTTACAAATGTGACGATGGAATCTGATAAGTACATCTGTGTTCGTGAGACTGCTCCACAAAACAGCGTGGTGATTATCGATATGAGCATGCCATCACAACCACTTCGGCGGCCCATTACAGCCGATTCAGCACTTATGAATCCAAATTCTAGAATTTTGGCATTGAAAGCTCAACTTCC...
LOC131020018
ATGGCGGCTGCCAATGCTCCGATCACCATGAAAGAAGCGCTTACGTTGACTAGCTTAGGGATCAATCCCCAGTTCATTACTTTTACAAATGTGACGATGGAATCTGATAAGTACATCTGTGTTCGTGAGACTGCTCCACAAAACAGCGTGGTGATTATCGATATGAGCATGCCATCACAACCACTTCGGCGGCCCATTACAGCCGATTCAGCACTTATGAATCCAAATTCTAGAATTTTGGCATTGAAAGCTCAACTTCC...

Protein

2 records

Download Protein FASTA
XP_057804631.1
MAAANAPITMKEALTLTSLGINPQFITFTNVTMESDKYICVRETAPQNSVVIIDMSMPSQPLRRPITADSALMNPNSRILALKAQLPGTTQDHLQIFNIEAKAKMKSHQMPEQVVFWKWITPKMLGLVTQSSVYHWSIEGDSEPVKMFDRTANLANNQIINYKCDPSEKWLVLIGIAPGSPERPQLVKGNMQLFSVDQQRSQALEAHAASFASFKIAGNDKDSILISFASKSSNAGQVTSKLHVIELGAQPGKPSFTKKQ...
XP_057804632.1
MAAANAPITMKEALTLTSLGINPQFITFTNVTMESDKYICVRETAPQNSVVIIDMSMPSQPLRRPITADSALMNPNSRILALKAQLPGTTQDHLQIFNIEAKAKMKSHQMPEQVVFWKWITPKMLGLVTQSSVYHWSIEGDSEPVKMFDRTANLANNQIINYKCDPSEKWLVLIGIAPGSPERPQLVKGNMQLFSVDQQRSQALEAHAASFASFKIAGNDKDSILISFASKSSNAGQVTSKLHVIELGAQPGKPSFTKKQ...

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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