PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Carubv10027519m
Common NameCARUB_v10027519mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family Trihelix
Protein Properties Length: 909aa    MW: 100451 Da    PI: 8.0899
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10027519mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix66.65.1e-21817897186
         trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                      +W+ +e+++ i++r e+++r++  k +++lWee+s++++++g++rsp qCk+ w +l ++y+++k+ e+++     +++p+f++++
  Carubv10027519m 817 KWKPEEIKKVIRMRGELHSRFQVVKGRMALWEEISSNLSAEGINRSPGQCKSLWASLVQKYEECKADERSK-----TSWPHFEDMN 897
                      7********************************************************************95.....36******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.5E-66106356IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.57E-72107521IPR001279Metallo-beta-lactamase
SMARTSM008493.0E-25119316IPR001279Metallo-beta-lactamase
PfamPF127065.2E-10131266IPR001279Metallo-beta-lactamase
PfamPF075215.5E-7461493IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.956810874IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.603.5E-5811876IPR009057Homeodomain-like
PfamPF138371.5E-17816898No hitNo description
CDDcd122031.01E-22816881No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009658Biological Processchloroplast organization
GO:0009942Biological Processlongitudinal axis specification
GO:0060918Biological Processauxin transport
GO:0009507Cellular Componentchloroplast
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 909 aa     Download sequence    Send to blast
MMKPASLQGF SSHVSSTIYS DVRRPATTPS KMAAFSALSL CPYTFTFRQS SRIKSTVSCS  60
VTSAPASGTS SSSKTPRRRR EGVGKSMEDS VKRKMEQFYE GTDGPPLRVL PIGGLGEIGM  120
NCMLVGNYDR YILIDAGIMF PDYDEPGVQK IMPDTGFIRR WKHQIEAVVI THGHEDHIGA  180
LPWVIPALDP NTPIFASSFT MELIKKRLKE HGIFVQSRLK TFSTRRRFMA GPFEIEPITV  240
THSIPDCSGL FLRCADGNIL HTGDWKIDEA PLDGKVFDRE ALEELSKEGV TLMMSDSTNV  300
LSPGRTISEK VVADALVRNV MAAKGRVITT QFASNIHRLG SIKAAADITG RKLVFVGMSL  360
RTYLEAAWRD GKAPIDPSSL VKVEDIEAYA PKELLIVTTG SQAEPRAALN LASYGSSHAF  420
KLTKEDIILY SAKVIPGNES RVMKMMNRLA DIGPNIIMGK NEMLHTSGHA YRGELEEVLK  480
IVKPQHFLPI HGELLFLKEH ELLGKSTGIR HTTVIKNGEM LGVSHLRNRR VLSNGFSSLG  540
RENLQLMYSD GDKAFGTSSE LCIDERLRIS SDGIIVLSME IMRPGVSENT LKGKIRITTR  600
CMWLDKGRLL DALHKAAHAA LSSCPVTCPL SHMERTVSEV LRKIVRKYSG KRPEVIAIAT  660
ENPMAVRADE VSARLSGDPS VGSGVVALRK VVDGHSKKSR PKKAPSQEDA PEEIDRTLED  720
DIIDSARLLA EEETAASTYA EEVKMPVGSS SEESDDFWKS FISPSSSPSP GETENVNKVT  780
DTEPKTEDKE SSRDDDNPSD TSDSETKPSS KRVRKNKWKP EEIKKVIRMR GELHSRFQVV  840
KGRMALWEEI SSNLSAEGIN RSPGQCKSLW ASLVQKYEEC KADERSKTSW PHFEDMNNIL  900
SELDTPAS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A5e-8810766119560RIBONUCLEASE J
5a0t_B5e-8810766119560RIBONUCLEASE J
5a0v_A5e-8810766119560RIBONUCLEASE J
5a0v_B5e-8810766119560RIBONUCLEASE J
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtEssential protein required during embryogenesis, especially in initiating and maintaining the organization of shoot apical meristems (SAMs), cotyledons, and hypocotyls (PubMed:15266054, PubMed:25871650). Involved in auxin-mediated pathways during embryogenesis (PubMed:25871650). RNase that has both endonuclease and 5'-3' exonuclease activities. Involved in RNA surveillance to prevent overaccumulation of antisense RNA (PubMed:22033332). Probably involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay (By similarity). {ECO:0000250|UniProtKB:Q72JJ7, ECO:0000269|PubMed:15266054, ECO:0000269|PubMed:22033332, ECO:0000269|PubMed:25871650}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10027519m
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By light. {ECO:0000269|PubMed:25871650}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2212720.0AK221272.1 Arabidopsis thaliana mRNA for putative protein, complete cds, clone: RAFL24-15-P14.
GenBankBT0042100.0BT004210.1 Arabidopsis thaliana clone RAFL16-01-C03 (R50172) unknown protein (At5g63420) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006279731.10.0uncharacterized protein LOC17874922
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLR0G7Y90.0R0G7Y9_9BRAS; Uncharacterized protein
STRINGXP_006279731.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95392634
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G63420.10.0Trihelix family protein
Publications ? help Back to Top
  1. Bryant N,Lloyd J,Sweeney C,Myouga F,Meinke D
    Identification of nuclear genes encoding chloroplast-localized proteins required for embryo development in Arabidopsis.
    Plant Physiol., 2011. 155(4): p. 1678-89
    [PMID:21139083]
  2. Halpert M,Liveanu V,Glaser F,Schuster G
    The Arabidopsis chloroplast RNase J displays both exo- and robust endonucleolytic activities.
    Plant Mol. Biol., 2019. 99(1-2): p. 17-29
    [PMID:30511330]