PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

RrC2335_p3

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

Trihelix

Protein Properties

Length: 1118aa MW: 123797 Da PI: 8.4912

Description

Trihelix family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC2335_p3	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	trihelix	61.8	1.6e-19	815	895	1	86
trihelix 1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 +W+ +ev++ i++r e+++r++ k +++lWee+s++++++g++rsp qCk+ w +l ++y+++k+ e+++ ++++++++++ RrC2335_p3 815 KWKPEEVKKVIRMRGELHSRFQVVKGRMALWEEISSNLSAEGINRSPGQCKSLWASLIQKYEECKADERSK-----TSWSHYEDMN 895 7******************************************************************95.....35999997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.60.15.10	9.4E-68	108	358	IPR001279	Metallo-beta-lactamase
SuperFamily	SSF56281	3.96E-72	109	523	IPR001279	Metallo-beta-lactamase
SMART	SM00849	5.2E-25	121	318	IPR001279	Metallo-beta-lactamase
Pfam	PF12706	1.3E-10	133	268	IPR001279	Metallo-beta-lactamase
Pfam	PF07521	6.3E-7	463	495	IPR011108	Zn-dependent metallo-hydrolase, RNA specificity domain
Gene3D	G3DSA:1.10.10.60	3.0E-5	808	874	IPR009057	Homeodomain-like
PROSITE profile	PS50090	8.107	808	872	IPR017877	Myb-like domain
Pfam	PF13837	9.2E-17	813	896	No hit	No description
CDD	cd12203	5.02E-22	814	879	No hit	No description
Gene3D	G3DSA:3.30.1200.10	2.8E-25	1018	1114	IPR003746	Protein of unknown function DUF167
SuperFamily	SSF69786	1.57E-17	1019	1105	IPR003746	Protein of unknown function DUF167
Hamap	MF_00634	14.538	1026	1114	IPR003746	Protein of unknown function DUF167
SMART	SM01152	8.3E-17	1026	1102	IPR003746	Protein of unknown function DUF167
Pfam	PF02594	1.3E-16	1030	1100	IPR003746	Protein of unknown function DUF167

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009658	Biological Process	chloroplast organization
GO:0009942	Biological Process	longitudinal axis specification
GO:0060918	Biological Process	auxin transport
GO:0009507	Cellular Component	chloroplast
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 1118 aa Download sequence Send to blast
MKPAASLQGY PSSSIYFDTR RPVPTPPSKM AAFSALSLSP YTFTFRQDSR LRPTVSCSVT 60 SPPASSGTSS SSKTPRRRSG RLEGAGKSME DSVKRKMEQF YEGTDGPPLR VLPIGGLGEI 120 GMNCMLVGNY DRYILIDAGI MFPDYDDPGV QKIMPDTGFI RRWKHKIEAV VITHGHEDHI 180 GALPWVIPAL DSNTPIFASS FTMELIKKRL KEHGIFVQSR LKTFNTRRRF MAGPFEVEPI 240 TVTHSIPDCS GLVLRCADGN ILHTGDWKID EAPLDGKVFD REALEELSKE GVTLMMSDST 300 NVLSPGRTTS EKVVADALVR NVMAAKGRVI TTQFASNIHR LGSIKAAADL TGRKLVFVGM 360 SLRTYLEAAW KDGKAPIDPS SLVKVEDIEA YSPKDLLIVT TGSQAEPRAA LNLASYGSSH 420 AFKLTKEDII LYSAKVIPGN ESRVMKMMNR LADIGPKIVM GKNEMLHTSG HAYRGELEEV 480 LKIVKPQHFL PIHGELLFLK EHELLGKSTG IRHTTVIKNG EMLGVSHLRN RRVLSNGFSS 540 LGRENLQLMY SDGDKAFGTA SELCIDERLR ISSDGIIVLS MEIMRPGVTE NTLKGKIRTT 600 TRCMWLDKGR LLDALHKAAH AALSSCPVNC PLSHMERTVS EVLRKIVRKY SGKRPEVIAI 660 AMENPMAVRA DEVSARMSGD PNLGSGVAAL RKVVEGNNKR NRTKKAPSQE EAGEIIDSSV 720 GLLGEEETTA SSSSYTEGAE DVPVRSSSEE SDDFWNSFIN PSSPSSPGET KRVDRLTDAE 780 TKTEDSESRR EEEEEEGDTS DSQTKSTTKR VRRNKWKPEE VKKVIRMRGE LHSRFQVVKG 840 RMALWEEISS NLSAEGINRS PGQCKSLWAS LIQKYEECKA DERSKTSWSH YEDMNNILSE 900 LDTPAPKYIE WGVRIQRFTS CSCLDTQLQK MPKRKTDRSS VLDKKKHLAR LNVSEGGKVL 960 LKRGEGKLER QFRMNCIGCE LFVCYRAEES LETASFIYIV DGALSAVAAE TNPQDAPVPP 1020 CISQLDGGLV QVAIEVEDRA QRSAITRVNA DDVRVTIAAP AARGEANNEL LEFMGRVLGL 1080 RLSQMTLQRG WNSKSKLLVV EDLSARQVYE KLLEAVAP

Sequence ? help Back to Top

Protein Sequence Length: 1118 aa Download sequence Send to blast

MKPAASLQGY PSSSIYFDTR RPVPTPPSKM AAFSALSLSP YTFTFRQDSR LRPTVSCSVT  60
SPPASSGTSS SSKTPRRRSG RLEGAGKSME DSVKRKMEQF YEGTDGPPLR VLPIGGLGEI  120
GMNCMLVGNY DRYILIDAGI MFPDYDDPGV QKIMPDTGFI RRWKHKIEAV VITHGHEDHI  180
GALPWVIPAL DSNTPIFASS FTMELIKKRL KEHGIFVQSR LKTFNTRRRF MAGPFEVEPI  240
TVTHSIPDCS GLVLRCADGN ILHTGDWKID EAPLDGKVFD REALEELSKE GVTLMMSDST  300
NVLSPGRTTS EKVVADALVR NVMAAKGRVI TTQFASNIHR LGSIKAAADL TGRKLVFVGM  360
SLRTYLEAAW KDGKAPIDPS SLVKVEDIEA YSPKDLLIVT TGSQAEPRAA LNLASYGSSH  420
AFKLTKEDII LYSAKVIPGN ESRVMKMMNR LADIGPKIVM GKNEMLHTSG HAYRGELEEV  480
LKIVKPQHFL PIHGELLFLK EHELLGKSTG IRHTTVIKNG EMLGVSHLRN RRVLSNGFSS  540
LGRENLQLMY SDGDKAFGTA SELCIDERLR ISSDGIIVLS MEIMRPGVTE NTLKGKIRTT  600
TRCMWLDKGR LLDALHKAAH AALSSCPVNC PLSHMERTVS EVLRKIVRKY SGKRPEVIAI  660
AMENPMAVRA DEVSARMSGD PNLGSGVAAL RKVVEGNNKR NRTKKAPSQE EAGEIIDSSV  720
GLLGEEETTA SSSSYTEGAE DVPVRSSSEE SDDFWNSFIN PSSPSSPGET KRVDRLTDAE  780
TKTEDSESRR EEEEEEGDTS DSQTKSTTKR VRRNKWKPEE VKKVIRMRGE LHSRFQVVKG  840
RMALWEEISS NLSAEGINRS PGQCKSLWAS LIQKYEECKA DERSKTSWSH YEDMNNILSE  900
LDTPAPKYIE WGVRIQRFTS CSCLDTQLQK MPKRKTDRSS VLDKKKHLAR LNVSEGGKVL  960
LKRGEGKLER QFRMNCIGCE LFVCYRAEES LETASFIYIV DGALSAVAAE TNPQDAPVPP  1020
CISQLDGGLV QVAIEVEDRA QRSAITRVNA DDVRVTIAAP AARGEANNEL LEFMGRVLGL  1080
RLSQMTLQRG WNSKSKLLVV EDLSARQVYE KLLEAVAP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5a0t_A	2e-84	109	663	19	560	RIBONUCLEASE J
5a0t_B	2e-84	109	663	19	560	RIBONUCLEASE J
5a0v_A	2e-84	109	663	19	560	RIBONUCLEASE J
5a0v_B	2e-84	109	663	19	560	RIBONUCLEASE J
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Functional Description ? help Back to Top
Source	Description
UniProt	Essential 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}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By light. {ECO:0000269\|PubMed:25871650}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK221272	0.0	AK221272.1 Arabidopsis thaliana mRNA for putative protein, complete cds, clone: RAFL24-15-P14.
GenBank	BT004210	0.0	BT004210.1 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
Refseq	XP_018432808.1	0.0	PREDICTED: uncharacterized protein LOC108805295
Swissprot	Q84W56	0.0	RNJ_ARATH; Ribonuclease J
TrEMBL	A0A3P5YIA8	0.0	A0A3P5YIA8_BRACM; Uncharacterized protein
STRING	Bo3g103450.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM9539	26	34

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G63420.1	0.0	Trihelix family protein

Publications ? help Back to Top
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] 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]