Basic Information
Locus ID:
Ag8G00007
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Clathrin is the major protein of the polyhedral coat of coated pits and vesicles
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr8 | 547695 | 562291 | + | Ag8G00007 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.22 | 193,274.53 Da | 41.27 | 97.64 | -0.14 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF00637 | Region in Clathrin and VPS | 701 | 840 | 3.9E-21 | IPR000547 |
| Pfam | PF00637 | Region in Clathrin and VPS | 850 | 983 | 8.8E-29 | IPR000547 |
| Pfam | PF00637 | Region in Clathrin and VPS | 557 | 690 | 7.1E-22 | IPR000547 |
| Pfam | PF00637 | Region in Clathrin and VPS | 1440 | 1579 | 1.0E-29 | IPR000547 |
| Pfam | PF00637 | Region in Clathrin and VPS | 993 | 1131 | 1.6E-30 | IPR000547 |
| Pfam | PF01394 | Clathrin propeller repeat | 156 | 197 | 1.4E-9 | IPR022365 |
| Pfam | PF01394 | Clathrin propeller repeat | 20 | 55 | 9.6E-7 | IPR022365 |
| Pfam | PF00637 | Region in Clathrin and VPS | 1289 | 1431 | 3.7E-29 | IPR000547 |
| Pfam | PF00637 | Region in Clathrin and VPS | 1147 | 1281 | 9.1E-26 | IPR000547 |
| Pfam | PF13838 | Clathrin-H-link | 369 | 434 | 7.3E-29 | - |
| Pfam | PF09268 | Clathrin, heavy-chain linker | 344 | 367 | 8.8E-9 | IPR015348 |
| SUPERFAMILY | SSF48371 | ARM repeat | 1196 | 1531 | 3.28E-105 | IPR016024 |
| SUPERFAMILY | SSF48371 | ARM repeat | 1050 | 1195 | 3.45E-27 | IPR016024 |
| SUPERFAMILY | SSF48371 | ARM repeat | 345 | 500 | 6.91E-53 | IPR016024 |
| SUPERFAMILY | SSF48371 | ARM repeat | 901 | 1066 | 2.33E-36 | IPR016024 |
| SUPERFAMILY | SSF50989 | Clathrin heavy-chain terminal domain | 5 | 343 | 1.83E-127 | IPR016025 |
| SUPERFAMILY | SSF48371 | ARM repeat | 457 | 793 | 1.64E-85 | IPR016024 |
| Gene3D | G3DSA:2.130.10.110 | - | 1 | 377 | 1.0E-157 | IPR016025 |
| Gene3D | G3DSA:1.25.40.10 | Tetratricopeptide repeat domain | 1197 | 1536 | 7.8E-163 | IPR011990 |
| Gene3D | G3DSA:1.25.40.10 | Tetratricopeptide repeat domain | 1056 | 1196 | 4.9E-26 | IPR011990 |
| Gene3D | G3DSA:1.25.40.10 | Tetratricopeptide repeat domain | 902 | 1055 | 6.1E-7 | IPR011990 |
| Gene3D | G3DSA:1.25.40.730 | - | 1542 | 1638 | 7.3E-41 | - |
| Gene3D | G3DSA:1.25.40.10 | Tetratricopeptide repeat domain | 459 | 788 | 1.2E-5 | IPR011990 |
| SMART | SM00299 | CLH_2 | 993 | 1138 | 6.1E-42 | IPR000547 |
| SMART | SM00299 | CLH_2 | 551 | 693 | 2.5E-34 | IPR000547 |
| SMART | SM00299 | CLH_2 | 847 | 986 | 1.2E-41 | IPR000547 |
| SMART | SM00299 | CLH_2 | 700 | 842 | 9.0E-39 | IPR000547 |
| SMART | SM00299 | CLH_2 | 1288 | 1434 | 2.5E-43 | IPR000547 |
| SMART | SM00299 | CLH_2 | 1142 | 1283 | 2.7E-35 | IPR000547 |
| SMART | SM00299 | CLH_2 | 1437 | 1596 | 3.7E-43 | IPR000547 |
| PIRSF | PIRSF002290 | CHC | 3 | 1679 | 0.0 | IPR016341 |
| ProSiteProfiles | PS50236 | Clathrin heavy-chain (CHCR) repeat profile. | 1288 | 1434 | 43.339775 | IPR000547 |
| ProSiteProfiles | PS50236 | Clathrin heavy-chain (CHCR) repeat profile. | 700 | 842 | 33.831902 | IPR000547 |
| ProSiteProfiles | PS50236 | Clathrin heavy-chain (CHCR) repeat profile. | 993 | 1138 | 42.789665 | IPR000547 |
| ProSiteProfiles | PS50236 | Clathrin heavy-chain (CHCR) repeat profile. | 551 | 697 | 36.607086 | IPR000547 |
| ProSiteProfiles | PS50236 | Clathrin heavy-chain (CHCR) repeat profile. | 1142 | 1283 | 33.519897 | IPR000547 |
| ProSiteProfiles | PS50236 | Clathrin heavy-chain (CHCR) repeat profile. | 1437 | 1580 | 39.242691 | IPR000547 |
| ProSiteProfiles | PS50236 | Clathrin heavy-chain (CHCR) repeat profile. | 847 | 986 | 36.910873 | IPR000547 |
| Coils | Coil | Coil | 1617 | 1652 | - | - |
Gene Ontology
Biological Process:
Molecular Function:
KEGG Pathway
KO Term:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G11130.1 | Clathrin, heavy chain. | 0 |
| RefSeq | XP_017222503.1 | PREDICTED: clathrin heavy chain 1-like [Daucus carota subsp. sativus] | 0 |
| Q0WNJ6 | Clathrin heavy chain 1 OS=Arabidopsis thaliana OX=3702 GN=CHC1 PE=1 SV=1 | 0 | |
| TrEMBL | A0A2J6KXU0 | Clathrin heavy chain OS=Lactuca sativa OX=4236 GN=LSAT_8X12740 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 27.190151 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 16.513357 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 15.275129 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 18.446136 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 19.458778 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 10.033635 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 11.39041 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 6.277721 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 38.276772 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 33.222725 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 37.295723 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 38.335316 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 35.884274 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 28.537022 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 13.162959 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 19.11421 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 15.905881 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 19.237926 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 14.681881 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 16.796019 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 18.050819 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 14.822621 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 13.604147 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 16.479008 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 15.134679 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 22.730963 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 16.714298 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 16.116573 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 22.140003 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 1.414219 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 2.376396 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 1.732987 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 2.950887 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 6.344872 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 3.028617 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 2.234132 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 0.998835 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 1.143169 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 22.135563 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 8.750557 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 5.033796 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 6.972793 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 8.525994 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 11.769337 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 9.014226 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 6.993141 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 10.052217 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 17.567097 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 17.748201 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 18.834045 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 3 | jg10038, jg14260, jg34119 |
| Aizoaceae | Mesembryanthemum crystallinum | 2 | gene_24312, gene_5770 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah027811 |
| Amaranthaceae | Beta vulgaris | 2 | BVRB_2g023550, BVRB_7g171840 |
| Amaranthaceae | Salicornia bigelovii | 4 | Sbi_jg1532, Sbi_jg21460, Sbi_jg22357, Sbi_jg35014 |
| Amaranthaceae | Salicornia europaea | 2 | Seu_jg16283, Seu_jg3217 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00016473 |
| Amaranthaceae | Suaeda glauca | 4 | Sgl62831, Sgl67446, Sgl72654, Sgl76192 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000017167, gene:ENSEOMG00000036403 ... |
| Amaranthaceae | Chenopodium quinoa | 4 | CQ.Regalona.r1.1BG0020030, CQ.Regalona.r1.2AG0021790 ... |
| Anacardiaceae | Pistacia vera | 3 | pistato.v30061210, pistato.v30065190, pistato.v30177160 |
| Apiaceae | Apium graveolens | 3 | Ag10G01296, Ag8G00007, Ag8G00430 |
| Arecaceae | Cocos nucifera | 2 | COCNU_04G003360, COCNU_12G006920 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103718112, gene-LOC103718217 |
| Asparagaceae | Asparagus officinalis | 2 | AsparagusV1_05.508.V1.1, AsparagusV1_07.439.V1.1 |
| Asteraceae | Flaveria trinervia | 3 | Ftri17G29926, Ftri18G15874, Ftri1G14408 |
| Brassicaceae | Arabidopsis thaliana | 2 | AT3G08530.1, AT3G11130.1 |
| Brassicaceae | Eutrema salsugineum | 3 | Thhalv10005737m.g.v1.0, Thhalv10019884m.g.v1.0 ... |
| Brassicaceae | Schrenkiella parvula | 2 | Sp3g07010.v2.2, Sp3g09440.v2.2 |
| Brassicaceae | Brassica nigra | 5 | BniB01g053920.2N, BniB01g055970.2N, BniB07g025160.2N ... |
| Casuarinaceae | Casuarina equisetifolia | 2 | Ceq02G0109, Ceq08G1851 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl02G0119, Cgl08G1908 |
| Cymodoceaceae | Cymodocea nodosa | 3 | gene.Cymno05g15190, gene.Cymno15g06980, gene.Cymno18g00690 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0114s00011.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 2 | gene.Thate01g27690, gene.Thate01g32470 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-8217 |
| Nitrariaceae | Nitraria sibirica | 2 | evm.TU.LG02.1892, evm.TU.LG02.2229 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00011784, Pov_00040538 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb3G19231, Lb3G20233 |
| Poaceae | Echinochloa crus-galli | 4 | AH04.22, AH05.100, BH04.29, CH04.29 |
| Poaceae | Eleusine coracana subsp. coracana | 4 | gene-QOZ80_5AG0378510, gene-QOZ80_5BG0425600 ... |
| Poaceae | Hordeum vulgare | 2 | HORVU.MOREX.r3.4HG0354730.1, HORVU.MOREX.r3.5HG0465820.1 |
| Poaceae | Lolium multiflorum | 5 | gene-QYE76_003751, gene-QYE76_027283, gene-QYE76_036738 ... |
| Poaceae | Oryza coarctata | 3 | Oco22G000070, Ocoptg000061lG000180, Ocoptg000463lG000010 |
| Poaceae | Oryza sativa | 2 | LOC_Os11g01380.1, LOC_Os12g01390.1 |
| Poaceae | Paspalum vaginatum | 2 | gene-BS78_05G003400, gene-BS78_08G001600 |
| Poaceae | Puccinellia tenuiflora | 3 | Pt_Chr0103585, Pt_Chr0103631, Pt_Chr0705210 |
| Poaceae | Sporobolus alterniflorus | 7 | Chr04G020700, Chr07G022460, Chr16G007860, Chr17G007090 ... |
| Poaceae | Thinopyrum elongatum | 2 | Tel4E01G211100, Tel5E01G265200 |
| Poaceae | Triticum dicoccoides | 5 | gene_TRIDC3AG073860, gene_TRIDC4AG029250 ... |
| Poaceae | Triticum aestivum | 6 | TraesCS4A02G182300.1, TraesCS4B02G136100.2 ... |
| Poaceae | Zea mays | 4 | Zm00001eb094250_P002, Zm00001eb163250_P001 ... |
| Poaceae | Zoysia japonica | 4 | nbis-gene-23331, nbis-gene-25848, nbis-gene-26945 ... |
| Poaceae | Zoysia macrostachya | 2 | Zma_g18320, Zma_g24589 |
| Portulacaceae | Portulaca oleracea | 6 | evm.TU.LG03.1799, evm.TU.LG05.153, evm.TU.LG14.80 ... |
| Posidoniaceae | Posidonia oceanica | 2 | gene.Posoc01g37080, gene.Posoc07g13940 |
| Rhizophoraceae | Bruguiera sexangula | 4 | evm.TU.Scaffold_11_RagTag.329, evm.TU.Scaffold_12_RagTag.112 ... |
| Rhizophoraceae | Carallia pectinifolia | 3 | nbisL1-mrna-14081, nbisL1-mrna-24686, nbisL1-mrna-30070 |
| Rhizophoraceae | Ceriops tagal | 3 | nbisL1-mrna-15482, nbisL1-mrna-15674, nbisL1-mrna-5993 |
| Rhizophoraceae | Ceriops zippeliana | 2 | nbisL1-mrna-16309, nbisL1-mrna-19418 |
| Rhizophoraceae | Kandelia candel | 3 | evm.TU.utg000005l.155, evm.TU.utg000015l.558 ... |
| Rhizophoraceae | Kandelia obovata | 3 | Maker00010105, Maker00015945, Maker00018225 |
| Rhizophoraceae | Rhizophora apiculata | 3 | nbisL1-mrna-446, nbisL1-mrna-4464, nbisL1-mrna-5494 |
| Rhizophoraceae | Rhizophora mangle | 3 | nbisL1-mrna-11646, nbisL1-mrna-18886, nbisL1-mrna-20843 |
| Salicaceae | Populus euphratica | 4 | populus_peu01746, populus_peu06568, populus_peu20447 ... |
| Solanaceae | Lycium barbarum | 3 | gene-LOC132609050, gene-LOC132637922, gene-LOC132640404 |
| Solanaceae | Solanum chilense | 2 | SOLCI004895900, SOLCI006013500 |
| Solanaceae | Solanum pennellii | 3 | gene-LOC107014039, gene-LOC107020217, gene-LOC107023023 |
| Tamaricaceae | Reaumuria soongarica | 2 | gene_10709, gene_3007 |
| Tamaricaceae | Tamarix chinensis | 2 | TC01G1157, TC11G1229 |
| Zosteraceae | Zostera marina | 3 | Zosma02g07230.v3.1, Zosma02g21680.v3.1, Zosma03g13790.v3.1 |