Basic Information
Locus ID:
Ag3G02533
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
zinc-ribbon
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr3 | 280675869 | 280676936 | + | Ag3G02533 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 4.83 | 27,984.10 Da | 45.24 | 73.56 | -0.46 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| Pfam | PF14369 | zinc-ribbon | 26 | 59 | 6.3E-9 | IPR039525 |
| Pfam | PF13639 | Ring finger domain | 179 | 220 | 3.2E-11 | IPR001841 |
| SUPERFAMILY | SSF57850 | RING/U-box | 174 | 226 | 5.98E-19 | - |
| Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain, C3HC4 (zinc finger) | 147 | 226 | 6.2E-18 | IPR013083 |
| SMART | SM00184 | ring_2 | 179 | 219 | 6.5E-8 | IPR001841 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 179 | 220 | 12.017182 | IPR001841 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 228 | 256 | - | - |
Gene Ontology
Molecular Function:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT5G64920.1 | COP1-interacting protein 8. Encodes a RING-H2 protein that interacts with the RING finger domain of COP1. CIP8 exhibits a strong interaction with the E2 ubiquitin conjugating enzyme AtUBC8 through its N-terminal domain and promotes ubiquitination in an E2-dependent fashion in vitro. It is possible that the AtUBC8-CIP8 module might interact with COP1 in vivo, thereby participating in proteasome-mediated degradation of HY5. | 0 |
| RefSeq | XP_017245726.1 | PREDICTED: E3 ubiquitin-protein ligase CIP8-like [Daucus carota subsp. sativus] | 0 |
| Q9SPL2 | E3 ubiquitin-protein ligase CIP8 OS=Arabidopsis thaliana OX=3702 GN=CIP8 PE=1 SV=1 | 0 | |
| TrEMBL | A0A165Y189 | RING-type domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_013877 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 53.793598 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 48.909214 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 58.725712 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 54.01255 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 58.236965 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 55.669174 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 51.317268 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 47.462048 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 86.714539 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 89.591919 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 89.463066 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 79.559578 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 81.002792 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 89.752037 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 74.717796 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 57.490562 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 78.38311 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 88.849792 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 76.247162 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 72.215912 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 89.341164 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 96.897797 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 84.207085 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 81.485741 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 90.583229 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 85.506454 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 78.642776 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 82.331734 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 76.626549 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 64.805344 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 49.224606 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 47.660316 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 203.25563 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 108.939857 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 223.598679 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 139.516098 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 96.088661 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 127.952972 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 77.036247 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 70.406128 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 51.29491 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 96.982956 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 117.451462 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 162.060638 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 158.468781 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 87.475082 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 126.465508 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 74.740402 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 65.097252 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 60.318806 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg10541, jg6355 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_8451 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah036218 |
| Amaranthaceae | Salicornia bigelovii | 2 | Sbi_jg40032, Sbi_jg55359 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg14301 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00014051 |
| Amaranthaceae | Suaeda glauca | 2 | Sgl12191, Sgl17563 |
| Amaranthaceae | Chenopodium album | 2 | gene:ENSEOMG00000016823, gene:ENSEOMG00000033883 |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.1AG0021160, CQ.Regalona.r1.1BG0003270 |
| Apiaceae | Apium graveolens | 1 | Ag3G02533 |
| Asteraceae | Flaveria trinervia | 4 | Ftri18G33999, Ftri1G22102, Ftri1G33111, Ftri8G11086 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT5G64920.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10005668m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp2g28000.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB03g033760.2N, BniB03g033770.2N |
| Casuarinaceae | Casuarina glauca | 1 | Cgl03G0948 |
| Plantaginaceae | Plantago ovata | 1 | Pov_00002567 |
| Poaceae | Echinochloa crus-galli | 2 | AH06.2374, BH06.2166 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_6AG0545610, gene-QOZ80_6BG0499100 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.7HG0722700.1.CDS1 |
| Poaceae | Lolium multiflorum | 1 | gene-QYE76_035157 |
| Poaceae | Oryza coarctata | 2 | Oco11G013330, Oco12G013470 |
| Poaceae | Oryza sativa | 1 | LOC_Os06g42700.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_10G199300 |
| Poaceae | Sporobolus alterniflorus | 2 | Chr10G018460, Chr11G004120 |
| Poaceae | Thinopyrum elongatum | 1 | Tel7E01G662300 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC7AG054450, gene_TRIDC7BG047190 |
| Poaceae | Triticum aestivum | 3 | TraesCS7A02G391700.1.cds1, TraesCS7B02G293600.1.cds1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb387590_P001 |
| Poaceae | Zoysia japonica | 2 | nbis-gene-40957, nbis-gene-9975 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g30851, Zma_g33102 |
| Portulacaceae | Portulaca oleracea | 5 | evm.TU.LG04.3350, evm.TU.LG12.1659, evm.TU.LG14.856 ... |
| Solanaceae | Lycium barbarum | 1 | gene-LOC132613824 |
| Solanaceae | Solanum chilense | 1 | SOLCI000622900 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107031553 |
| Tamaricaceae | Reaumuria soongarica | 1 | STRG.31285_chr11_+ |
| Tamaricaceae | Tamarix chinensis | 1 | TC04G2884 |