Basic Information
Locus ID:
Ag3G01537
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
lysine-specific demethylase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr3 | 96823824 | 96836023 | - | Ag3G01537 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.23 | 151,396.05 Da | 43.23 | 68.89 | -0.85 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd02208 | cupin_RmlC-like | 1184 | 1244 | 2.67197E-5 | - |
| Pfam | PF02373 | JmjC domain, hydroxylase | 1144 | 1243 | 5.5E-15 | IPR003347 |
| SUPERFAMILY | SSF51197 | Clavaminate synthase-like | 839 | 1292 | 1.06E-34 | - |
| Gene3D | G3DSA:2.60.120.650 | Cupin | 824 | 1269 | 4.9E-160 | - |
| SMART | SM00558 | cupin_9 | 941 | 1260 | 2.7E-72 | IPR003347 |
| ProSiteProfiles | PS51184 | JmjC domain profile. | 960 | 1260 | 29.010397 | IPR003347 |
| ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 523 | 570 | 8.520721 | IPR001841 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 304 | 414 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 28 | 66 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 386 | 414 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 266 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 324 | 342 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 349 | 376 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 459 | 480 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1298 | 1336 | - | - |
| Coils | Coil | Coil | 407 | 427 | - | - |
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT3G07610.1 | Transcription factor jumonji (jmjC) domain-containing protein. IBM1 likely encodes a protein with histone H3mK9 demethylation activity. It may preferentially demethylate H3mK9 at low-copy loci to protect them from silencing by nearby heterochromatin by preventing the spread of cytosine methylation. BONSAI (At1g73177) is hypermethylated in ibm1 mutants. ibm1 mutants have morphological defects that become apparent at the F3 generation, including small narrow leaves, arrested flower development, and faulty pollen development. These phenotypes cannot result solely from the BONSAI hypermethylation. Aberrant phenotypes in ibm1 mutants in both DNA methylation and plant development can be suppressed by mutations in the KYP H3K9 methyltransferase or he CMT3 non CG-cytosine methylase. | 0 |
| RefSeq | XP_017247225.1 | PREDICTED: lysine-specific demethylase JMJ25-like [Daucus carota subsp. sativus] | 0 |
| Q9SSE9 | Lysine-specific demethylase JMJ25 OS=Arabidopsis thaliana OX=3702 GN=JMJ25 PE=1 SV=1 | 0 | |
| TrEMBL | A0A6L5BAV2 | Rep_fac-A_C domain-containing protein OS=Apium graveolens OX=4045 GN=AG4045_008777 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 14.598594 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 9.191306 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 10.366271 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 12.610445 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 12.056143 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 9.052296 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 11.829436 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 8.112614 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 16.662708 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 15.735265 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 17.140749 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 15.323904 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 15.297435 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 12.07498 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 4.224979 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 6.764959 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 4.917546 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 6.695607 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 4.235012 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 5.144248 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 5.291819 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 6.015618 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 5.751485 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 6.342273 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 5.897121 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 10.006241 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 4.821591 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 6.167103 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 8.874804 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 1.464219 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 2.088409 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 1.039316 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 2.385057 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 2.019959 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 2.02424 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 0.795636 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 0.90674 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 0.723193 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 6.276298 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 3.250954 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 3.835258 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 11.554465 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 17.635746 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 9.328107 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 10.708775 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 9.884965 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 9.459695 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 6.390442 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 6.611341 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 6.67587 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology