PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Rsa1.0_02987.1_g00006.1
Organism
Raphanus sativus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family B3
Protein Properties Length: 730aa    MW: 81552.6 Da    PI: 9.1288
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_02987.1_g00006.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B348.31.8e-15170254190
                              EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                       B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                              f  vl ps+  + ++++lp  fae++ +g++ + +++   ++  ++W v++    k gr  +++GW eF  +n+L egD++vF+l 
  Rsa1.0_02987.1_g00006.1 170 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKV---QLGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNLGEGDVCVFELL 249
                              677899********************84442.43344...4677*******..666666779**********************99 PP

                              SSSEE CS
                       B3  86 grsef 90 
                              ++++f
  Rsa1.0_02987.1_g00006.1 250 RTRDF 254
                              88777 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.7E-21162256IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.12E-21165260IPR015300DNA-binding pseudobarrel domain
CDDcd100173.13E-18168251No hitNo description
PROSITE profilePS5086311.885170262IPR003340B3 DNA binding domain
PfamPF023628.0E-14170254IPR003340B3 DNA binding domain
SMARTSM010195.4E-19170262IPR003340B3 DNA binding domain
PROSITE profilePS513757.936407441IPR002885Pentatricopeptide repeat
TIGRFAMsTIGR007569.9E-4412437IPR002885Pentatricopeptide repeat
PfamPF015350.0014412437IPR002885Pentatricopeptide repeat
PfamPF015350.093440452IPR002885Pentatricopeptide repeat
PROSITE profilePS513756.127480514IPR002885Pentatricopeptide repeat
PROSITE profilePS513756.906517547IPR002885Pentatricopeptide repeat
PfamPF130413.1E-7547594IPR002885Pentatricopeptide repeat
PROSITE profilePS5137510.008548582IPR002885Pentatricopeptide repeat
TIGRFAMsTIGR007560.0018551584IPR002885Pentatricopeptide repeat
PROSITE profilePS513759.35583613IPR002885Pentatricopeptide repeat
TIGRFAMsTIGR007564.4E-4585618IPR002885Pentatricopeptide repeat
PROSITE profilePS513755.886619649IPR002885Pentatricopeptide repeat
PROSITE profilePS513757.509689723IPR002885Pentatricopeptide repeat
PfamPF015350.047693721IPR002885Pentatricopeptide repeat
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0080156Biological Processmitochondrial mRNA modification
GO:0005739Cellular Componentmitochondrion
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 730 aa     Download sequence    Send to blast
YEGNSAFSVY IYNLSHSEIN YHSSGLMDTP HNHLKRARLF EDLEDEDAAA EVVVYSSSSS  60
VYPPSSHHPG VTVAVNKGYA SSSPAIQSFF AGPVKAEETT PTPKVAKKRG RKKKNAVPEE  120
INSSAPRDDD PESRSKFYES ASARKRTVTA EERERAINAA KTFEPTNPFF RVVLRPSYLY  180
RGCIMYLPSG FAEKYLSGIS GFIKVQLGEK QWPVRCLYKA GRAKFSQGWY EFTLENNLGE  240
GDVCVFELLR TRDFVLKNFV VPMSSVFPGP RFLSLLQRNT KTLVQAKQIH AQLVINGCFR  300
DNSLLGKLIG HYCSNQSTES SKLAHSLAFP RFSRPDKFLF NTLLKCSNPE DSIRIFTNWA  360
SKSSLLYLNE RTFVFLLGAC ARSASSSSGV GRMVHGMVMK LGFLHNSELI GTTLLHFYAK  420
HGDLRYARKV FDEMPERTSV TWNAMIGGYC SRKDKGNHNA RKGMILFRRF SSCGDGVRPT  480
DTTMVCVLSA ISQMGLLEVG ALVHGYVEKL GFTPEVDVFI GTGLVDMYSK CGCLTSAISV  540
FELMRVKNVL TWTSMATGLA LSGRGSETPS LLNRMAESGI RPNEVTFTSL LSAYRHIGLV  600
QEGLELFRSM RTRFGVTPVI QHYGCVVDLL GKAGRLREAY EFVLAMPIKP DSIMLRSLCN  660
ACSIYGETVM GEEIGKALME MEQEEKGCEC EDYVALSNVF ASKGKWVEVE KLRNEMRERR  720
IKTRPGYSFV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-8213325712136B3 domain-containing transcription factor VRN1
4i1k_B1e-8213325712136B3 domain-containing transcription factor VRN1
Search in ModeBase
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_02987.1_g00006.1
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2325620.0AC232562.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH054E04, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018492007.10.0PREDICTED: pentatricopeptide repeat-containing protein At3g18970
SwissprotQ9LJ690.0PP243_ARATH; Pentatricopeptide repeat-containing protein At3g18970
TrEMBLM4E0S80.0M4E0S8_BRARP; Uncharacterized protein
STRINGBra022375.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM1281033
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G18990.11e-133B3 family protein
Publications ? help Back to Top
  1. Lurin C, et al.
    Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis.
    Plant Cell, 2004. 16(8): p. 2089-103
    [PMID:15269332]
  2. Takenaka M,Verbitskiy D,Zehrmann A,Brennicke A
    Reverse genetic screening identifies five E-class PPR proteins involved in RNA editing in mitochondria of Arabidopsis thaliana.
    J. Biol. Chem., 2010. 285(35): p. 27122-9
    [PMID:20566637]
  3. Liu JM, et al.
    The E-Subgroup Pentatricopeptide Repeat Protein Family in Arabidopsis thaliana and Confirmation of the Responsiveness PPR96 to Abiotic Stresses.
    Front Plant Sci, 2016. 7: p. 1825
    [PMID:27994613]