PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
|
Home TFext BLAST Prediction Download Help About Links PlantRegMap |
Transcription Factor Information
Basic Information? help Back to Top | |||||||||
---|---|---|---|---|---|---|---|---|---|
TF ID | IGS.gm_22_00195 | ||||||||
Common Name | CHLNCDRAFT_138954 | ||||||||
Organism | |||||||||
Taxonomic ID | |||||||||
Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Chlorophyta; Trebouxiophyceae; Chlorellales; Chlorellaceae; Chlorella
|
||||||||
Family | C3H | ||||||||
Protein Properties | Length: 234aa MW: 25317.5 Da PI: 8.1323 | ||||||||
Description | C3H family protein | ||||||||
Gene Model |
|
Signature Domain? help Back to Top | |||||||
---|---|---|---|---|---|---|---|
No. | Domain | Score | E-value | Start | End | HMM Start | HMM End |
1 | zf-CCCH | 17.7 | 6.4e-06 | 103 | 118 | 9 | 25 |
GGGTS--TTTTT-SS-S CS zf-CCCH 9 fartGtCkyGdrCkFaH 25 + G+C yG+ C+F H IGS.gm_22_00195 103 YKL-GFCIYGPACRFKH 118 555.************* PP |
Protein Features ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Database | Entry ID | E-value | Start | End | InterPro ID | Description |
Gene3D | G3DSA:4.10.1000.10 | 2.8E-6 | 36 | 65 | IPR000571 | Zinc finger, CCCH-type |
SuperFamily | SSF90229 | 2.88E-7 | 40 | 65 | IPR000571 | Zinc finger, CCCH-type |
SMART | SM00356 | 2.7E-5 | 40 | 66 | IPR000571 | Zinc finger, CCCH-type |
PROSITE profile | PS50103 | 13.526 | 40 | 67 | IPR000571 | Zinc finger, CCCH-type |
SMART | SM00356 | 0.56 | 68 | 94 | IPR000571 | Zinc finger, CCCH-type |
PROSITE profile | PS50103 | 8.23 | 68 | 92 | IPR000571 | Zinc finger, CCCH-type |
PROSITE profile | PS50103 | 11.253 | 94 | 121 | IPR000571 | Zinc finger, CCCH-type |
SMART | SM00356 | 0.058 | 96 | 120 | IPR000571 | Zinc finger, CCCH-type |
Gene3D | G3DSA:4.10.1000.10 | 3.0E-4 | 100 | 121 | IPR000571 | Zinc finger, CCCH-type |
Gene Ontology ? help Back to Top | ||||||
---|---|---|---|---|---|---|
GO Term | GO Category | GO Description | ||||
GO:0006979 | Biological Process | response to oxidative stress | ||||
GO:0034052 | Biological Process | positive regulation of plant-type hypersensitive response | ||||
GO:1900363 | Biological Process | regulation of mRNA polyadenylation | ||||
GO:2000031 | Biological Process | regulation of salicylic acid mediated signaling pathway | ||||
GO:0005634 | Cellular Component | nucleus | ||||
GO:0005737 | Cellular Component | cytoplasm | ||||
GO:0003723 | Molecular Function | RNA binding | ||||
GO:0004521 | Molecular Function | endoribonuclease activity | ||||
GO:0005516 | Molecular Function | calmodulin binding | ||||
GO:0046872 | Molecular Function | metal ion binding |
Sequence ? help Back to Top |
---|
Protein Sequence Length: 234 aa Download sequence Send to blast |
MDDFTFDFER GLESQPAQRG YQAADDGMGG RGNAEPKPRN YRQTVCTYWL RGLCMKGDTC 60 GFLHQFDPER MPVCRSLLKF GVCKEPDCPY KHTLEAIKEC NMYKLGFCIY GPACRFKHTR 120 QLAPPPDPET LEAAKPREHR NLNIVANQAN ENIMPEREAR GPRRPRPGGD GGGYMALPGA 180 GGGGGAGPSA VQQYAGPGGA RQPGQQYGGQ QAPGYADSAL LAAVGQADLR YGF* |
3D Structure ? help Back to Top | ||||||
---|---|---|---|---|---|---|
PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
6dnh_C | 1e-20 | 42 | 122 | 65 | 147 | Cleavage and polyadenylation specificity factor subunit 4 |
6fbs_C | 1e-20 | 42 | 123 | 64 | 147 | Cleavage and polyadenylation specificity factor subunit 4 |
6fuw_C | 1e-20 | 42 | 123 | 64 | 147 | Cleavage and polyadenylation specificity factor subunit 4 |
Search in ModeBase |
Functional Description ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Source | Description | |||||
UniProt | Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation. May interact with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition (By similarity). Mediates poly(A) site selection (PubMed:23136375). Binds RNA in a calcium-dependent manner (PubMed:16500995, PubMed:17576667, PubMed:20214900). Exhibits endonuclease activity with an ability to nick and degrade linear as well as circular single-stranded RNA that leaves RNA 3' ends with hydroxyl groups, thus mediating processing of the pre-mRNA as a prelude to the polyadenylation (PubMed:17576667). Involved in the post-transcriptional control, probably via poly(A) addition, of the responses of plants to stress, especially genes mediating tolerance to oxidative stress (PubMed:18545667). Plays a role in the regulation of salicylic acid (SA) production via the control of messenger RNA 3' end processing, thus being a key component of programmed cell death and plant immune responses required for resistance to virulent Pseudomonas syringae pv tomato DC3000 (Pst) (PubMed:24706550). {ECO:0000250|UniProtKB:O95639, ECO:0000269|PubMed:16500995, ECO:0000269|PubMed:17576667, ECO:0000269|PubMed:18545667, ECO:0000269|PubMed:20214900, ECO:0000269|PubMed:23136375, ECO:0000269|PubMed:24706550}. |
Regulation -- Description ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Source | Description | |||||
UniProt | INDUCTION: Isoform 2 is up-regulated by exposure to the oxidative agent methyl viologen (MV). {ECO:0000269|PubMed:18545667}. |
Annotation -- Protein ? help Back to Top | |||||||
---|---|---|---|---|---|---|---|
Source | Hit ID | E-value | Description | ||||
Refseq | XP_005844535.1 | 1e-171 | hypothetical protein CHLNCDRAFT_138954 | ||||
Swissprot | A9LNK9 | 3e-37 | CPSF_ARATH; 30-kDa cleavage and polyadenylation specificity factor 30 | ||||
TrEMBL | E1ZP09 | 1e-169 | E1ZP09_CHLVA; Uncharacterized protein | ||||
STRING | XP_005844535.1 | 1e-170 | (Chlorella variabilis) |
Orthologous Group ? help Back to Top | |||
---|---|---|---|
Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Chlorophytae | OGCP3492 | 7 | 7 |
Best hit in Arabidopsis thaliana ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Hit ID | E-value | Description | ||||
AT3G06410.1 | 9e-06 | C3H family protein |
Link Out ? help Back to Top | |
---|---|
Entrez Gene | 17351970 |