RubberDandelionOmics Rubber Dandelion Multi-omics Website
More
Transcriptome Expression Annotation Rubber Pathway TF Prediction Targets Protein Network Resequencing Tools Downloads
ZH EN

How to use this page

Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_021841
Reference: OH-1004 Chr: Chr04 Coordinates: 138427164-138437845 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

5112 bp · LXL04_021841|LXL04_021841|OH1004|cDNA

ATGGCGGCCGCGAACGCTCCAATTACTATGAAAGAGGCACTCACGTTGCCTAGCGTGGGGATCAATCCTCAGTTTATTACGTTCACCAATGTGACAATGGAGTCAGATAAGTACATTTGCGTTCGAGAAACATCTCCTCAGAATAGTGTGGTGATTATCGATATGAGCATGCCTATGCAGCCACTGAGGAGACCAATTACTGCTGACTCAGCTCTTATGAATCCTGTTTCCAAGATACTGGCTCTAAAAGCTCAACTGCC...

CDS

Download CDS FASTA

5112 bp · LXL04_021841|LXL04_021841|OH1004|CDS

ATGGCGGCCGCGAACGCTCCAATTACTATGAAAGAGGCACTCACGTTGCCTAGCGTGGGGATCAATCCTCAGTTTATTACGTTCACCAATGTGACAATGGAGTCAGATAAGTACATTTGCGTTCGAGAAACATCTCCTCAGAATAGTGTGGTGATTATCGATATGAGCATGCCTATGCAGCCACTGAGGAGACCAATTACTGCTGACTCAGCTCTTATGAATCCTGTTTCCAAGATACTGGCTCTAAAAGCTCAACTGCC...

Protein

Download Protein FASTA

1703 aa · LXL04_021841|LXL04_021841|OH1004|PROTEIN

MAAANAPITMKEALTLPSVGINPQFITFTNVTMESDKYICVRETSPQNSVVIIDMSMPMQPLRRPITADSALMNPVSKILALKAQLPGTTQDHLQIFNIEMKAKMKSHQMPEQVVFWKWITPKMLGMVTQTSVYHWSIEGDSEPTKMFDRTANLSNNQIINYRCDPSEKWLVLIGITPGSPERPQLVKGNMQLFSVDQQRSQALEAHAASFASFKVPGNENPSILISFATKSSNAGQVTSKLHVIELGAQPGKPSFTKKQ...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

Download Gene (CDS) Download Protein

ID Mapping

Input IDLXL04_021841
TK1151 IDTkA05G428790
OH-1004 IDLXL04_021841
Relationship / confidenceNon Reciprocal Best Hit / Complex relationship
Protein identity (%)99.600
Protein coverage (%)TK1151 97.843 / OH-1004 66.588
Coverage and evidence

Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.

Source versionOH-1004 / GCA_047496595.1_OSU_TarKok_2.0
Open Full ID Mapping
SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene IDLXL04_021841
LocationChr04:138427164-138437845 (-)
DescriptionSimilar to CHC1: Clathrin heavy chain 1
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g11130 Clathrin is the major protein of the polyhedral coat of coated pits and vesicles (By similarity). No verified direct reference in this release
At3g08530 Clathrin is the major protein of the polyhedral coat of coated pits and vesicles (By similarity).
Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis.2011 · DOI: 10.1105/tpc.111.083030

Rice

Reference gene IDPossible functionPapers / DOI
Os11g0104900 Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. No verified direct reference in this release
Os12g0104800 Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_021841 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0000278 mitotic cell cycle Biological Process
GO:0006886 intracellular protein transport Biological Process
GO:0006897 endocytosis Biological Process
GO:0006898 receptor-mediated endocytosis Biological Process
GO:0006914 autophagy Biological Process
GO:0007030 Golgi organization Biological Process
GO:0009414 response to water deprivation Biological Process
GO:0010118 stomatal movement Biological Process
GO:0016192 vesicle-mediated transport Biological Process
GO:0031623 receptor internalization Biological Process
GO:0033572 transferrin transport Biological Process
GO:0042147 retrograde transport, endosome to Golgi Biological Process
KEGG gene cross-reference
ath:AT3G08530
ath:AT3G11130
mmu:67300
osa:4349546
osa:4351255
These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.
Open Annotation Module

Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene
Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Cytoplasm0.708
Rank 1 · LXL04_021841 · OH-1004
Nucleus0.226
Rank 2 · LXL04_021841 · OH-1004
Cell membrane0.175
Rank 3 · LXL04_021841 · OH-1004
Lysosome / Vacuole0.112
Rank 4 · LXL04_021841 · OH-1004
Golgi apparatus0.109
Rank 5 · LXL04_021841 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF01394.27Clathrin_propel20-55 aa
PF01394.27Clathrin_propel155-197 aa
PF09268.17Clathrin-link344-367 aa
PF13838.13Clathrin_H_link369-434 aa
PF00637.27Clathrin557-692 aa
PF00637.27Clathrin701-841 aa
PF00637.27Clathrin850-984 aa
PF00637.27Clathrin993-1131 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_021841PF01394.27Clathrin_propel20551.3e-35120.4
LXL04_021841PF01394.27Clathrin_propel1551971.3e-35120.4
LXL04_021841PF09268.17Clathrin-link3443673e-0936.7
LXL04_021841PF13838.13Clathrin_H_link3694341.1e-2899.7
LXL04_021841PF00637.27Clathrin5576921.5e-214703.1
LXL04_021841PF00637.27Clathrin7018411.5e-214703.1
LXL04_021841PF00637.27Clathrin8509841.5e-214703.1
LXL04_021841PF00637.27Clathrin99311311.5e-214703.1
LXL04_021841PF00637.27Clathrin114412811.5e-214703.1
LXL04_021841PF00637.27Clathrin128814321.5e-214703.1
LXL04_021841PF00637.27Clathrin143815791.5e-214703.1

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q0WNJ6Arabidopsis thalianaClathrin heavy chain 192.637%Swiss-Protstrong database homology
Q0WLB5Arabidopsis thalianaClathrin heavy chain 292.275%Swiss-Protstrong database homology
Q2RBN7Oryza sativa subsp. japonicaClathrin heavy chain 191.249%Swiss-Protstrong database homology
Q2QYW2Oryza sativa subsp. japonicaClathrin heavy chain 291.249%Swiss-Protstrong database homology

JBrowse

View in Genome Browser