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

Itr_sc002017.1_g00002.1

Organism

Ipomoea trifida

Taxonomic ID

35884

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea

Family

Trihelix

Protein Properties

Length: 1560aa MW: 174404 Da PI: 8.6416

Description

Trihelix family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Itr_sc002017.1_g00002.1	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	trihelix	62.2	1.2e-19	1468	1548	1	86
trihelix 1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdq 84 +W+ +ev++Li++r e++++++ k +++lW+e+s+++ + g++rsp qCk+ w +l ++y++ k+ +k+ ++++pyf++ Itr_sc002017.1_g00002.1 1468 KWKPEEVKKLIKMRGELNSKFQVLKGRMALWQEISSNLLSDGVSRSPGQCKSLWASLVQKYEESKKDRKS-----QEKWPYFKD 1546 7**************************************************************99998.....478**** PP trihelix 85 le 86 ++ Itr_sc002017.1_g00002.1 1547 MD 1548 *8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF00078	3.1E-13	53	173	IPR000477	Reverse transcriptase domain
Pfam	PF13966	3.2E-18	370	460	IPR026960	Reverse transcriptase zinc-binding domain
Pfam	PF13456	1.1E-16	522	633	No hit	No description
CDD	cd06222	2.63E-19	525	633	No hit	No description
Gene3D	G3DSA:3.60.15.10	4.0E-65	726	981	IPR001279	Metallo-beta-lactamase
SuperFamily	SSF56281	5.76E-68	727	1134	IPR001279	Metallo-beta-lactamase
SMART	SM00849	2.2E-24	739	941	IPR001279	Metallo-beta-lactamase
Pfam	PF00753	3.5E-9	740	892	IPR001279	Metallo-beta-lactamase
Pfam	PF07521	3.9E-6	1086	1118	IPR011108	Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profile	PS50090	8.223	1461	1525	IPR017877	Myb-like domain
Gene3D	G3DSA:1.10.10.60	6.8E-5	1462	1527	IPR009057	Homeodomain-like
Pfam	PF13837	1.9E-17	1466	1550	No hit	No description
CDD	cd12203	2.83E-19	1467	1532	No hit	No description

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: 1560 aa Download sequence Send to blast
MAPEKAPGPD GMSPSFFQHF WPIVGHDLYM FVVNCLNTCT FPKGLNDTNI ILIPKKKVHV 60 KVSDLRPIAL CNVAYKVMTK VLANRMKGIL NVIISPTQSA FVAGEVRHFL RRKCNGNVGW 120 AALKLDIAKA YDRMEWCFLE GMLVALGFNR RWVDLLMLCV KSKDYPCCYN GLRLGVISMA 180 LGLHVELRLI SKAGREVLIK SIAQSLPVFT MSVYLLPASV CDTIEKVLNR YWWSGGGDRQ 240 KGIHWLTKQG WHLLTNPDSL VGRLLKAKYF PRWQHVLKLG VARTIGDGVD TKVWGWPWLY 300 DSVNPFLQTP VIDELKEAAV CSLFDGHGNW DLEILHDLFE PVDVQRVLAT PISLHSKDYW 360 RWLGDIRGVY TVKNSYALLT AQNTVVDGSC VFSAWDKIWK LPIPPNVRNF LWRCARNIIP 420 VKEVLKQKHV YIGGGCPLCA NAEESVEHLF FSCVVASQIW GDHNVLQGKT LHEFMQLTLS 480 SPDVDKAVRM VAIFWVLWSV RNEKIWHNGF RTAESINMQI QRDGAGFGAV LRDHVGRFVA 540 AKYDRLPTVR DPFMAEALAV KEAMSWLKDI GQANIILETY CLNFCLAFNS RTVNLSYVGV 600 IVTHCRSLAR DIGNVSVHHV KRLANHVAHV LARATGSSAG LGSWDLISPD CIADSSVSLC 660 PYKLWYQPHL RRRFVSCSVR TPSVKDIRGA KLPRKRNVKG EGVGKSMEDA VQRKMEQFYE 720 GSDGPPLRIL PIGGLGEIGM NCMLVGYYDR YILIDAGVMF PGYDELGVVK IIPDTTFIEK 780 WSHKIEAVVI THGHEDHIGA LPWFTGIQVI PALDSGTPIF ASSFTLELIK KRLKEFSIFV 840 PSRLKVFKTR RRFTAGPFEV EPIRVTHSIP DCCGLVLRCD AGTILHTGDW KIDESPLDGN 900 VFDREALEEL SKEGVTLMMS DSTNVLSPGR TLSETVVADS LLRHISAATG RIIATQFASN 960 IHRLGSMKAA ADLTGRKLVF VGMSLRTYLD AAWKAGKAPI DPSTLVKAED IDSYAPKDLL 1020 IVTTGSQAEP RAALNLASYG SSHSLKLSKE DLILYSAKVI PGNETRVMKM LNRISEIGST 1080 VIMGKNELLH TSGHGHREEL EEVLRIVKPQ HFLPIHGELL FLKEHELLGR STGIRHSTAP 1140 LMEASTQFLV FWLPLSLFFD QVIKNGEMLG VSHLRNRRVL SNGFISLGKE NLQLMYSDGD 1200 KAFGTAAELC VDERMRIASD GIIVVSMEIL RPQPSDTLSE KVIKGKIRIT TRCLWLDKGK 1260 LLDALHKAAH AALSSCPVNC PLHHIERTVS EVLRKLVRKY SSKRPEVIAI AIENPVSVLA 1320 DEINGKLSGK SHVGSGISVL RKAINGDQEK RWSNTTQAEE DNVPEHLMNI AYEEEKGTDI 1380 DIERDTSGEE TTSSSLLQDC SNNDLPSDDF WKPFVTSSTI HPSEENGDGD GSLLQEQLHD 1440 SSVKGNNILF SDVSKSKLKS SKSMTRNKWK PEEVKKLIKM RGELNSKFQV LKGRMALWQE 1500 ISSNLLSDGV SRSPGQCKSL WASLVQKYEE SKKDRKSQEK WPYFKDMDNI LSDLEAPASK

Sequence ? help Back to Top

Protein Sequence Length: 1560 aa Download sequence Send to blast

MAPEKAPGPD GMSPSFFQHF WPIVGHDLYM FVVNCLNTCT FPKGLNDTNI ILIPKKKVHV  60
KVSDLRPIAL CNVAYKVMTK VLANRMKGIL NVIISPTQSA FVAGEVRHFL RRKCNGNVGW  120
AALKLDIAKA YDRMEWCFLE GMLVALGFNR RWVDLLMLCV KSKDYPCCYN GLRLGVISMA  180
LGLHVELRLI SKAGREVLIK SIAQSLPVFT MSVYLLPASV CDTIEKVLNR YWWSGGGDRQ  240
KGIHWLTKQG WHLLTNPDSL VGRLLKAKYF PRWQHVLKLG VARTIGDGVD TKVWGWPWLY  300
DSVNPFLQTP VIDELKEAAV CSLFDGHGNW DLEILHDLFE PVDVQRVLAT PISLHSKDYW  360
RWLGDIRGVY TVKNSYALLT AQNTVVDGSC VFSAWDKIWK LPIPPNVRNF LWRCARNIIP  420
VKEVLKQKHV YIGGGCPLCA NAEESVEHLF FSCVVASQIW GDHNVLQGKT LHEFMQLTLS  480
SPDVDKAVRM VAIFWVLWSV RNEKIWHNGF RTAESINMQI QRDGAGFGAV LRDHVGRFVA  540
AKYDRLPTVR DPFMAEALAV KEAMSWLKDI GQANIILETY CLNFCLAFNS RTVNLSYVGV  600
IVTHCRSLAR DIGNVSVHHV KRLANHVAHV LARATGSSAG LGSWDLISPD CIADSSVSLC  660
PYKLWYQPHL RRRFVSCSVR TPSVKDIRGA KLPRKRNVKG EGVGKSMEDA VQRKMEQFYE  720
GSDGPPLRIL PIGGLGEIGM NCMLVGYYDR YILIDAGVMF PGYDELGVVK IIPDTTFIEK  780
WSHKIEAVVI THGHEDHIGA LPWFTGIQVI PALDSGTPIF ASSFTLELIK KRLKEFSIFV  840
PSRLKVFKTR RRFTAGPFEV EPIRVTHSIP DCCGLVLRCD AGTILHTGDW KIDESPLDGN  900
VFDREALEEL SKEGVTLMMS DSTNVLSPGR TLSETVVADS LLRHISAATG RIIATQFASN  960
IHRLGSMKAA ADLTGRKLVF VGMSLRTYLD AAWKAGKAPI DPSTLVKAED IDSYAPKDLL  1020
IVTTGSQAEP RAALNLASYG SSHSLKLSKE DLILYSAKVI PGNETRVMKM LNRISEIGST  1080
VIMGKNELLH TSGHGHREEL EEVLRIVKPQ HFLPIHGELL FLKEHELLGR STGIRHSTAP  1140
LMEASTQFLV FWLPLSLFFD QVIKNGEMLG VSHLRNRRVL SNGFISLGKE NLQLMYSDGD  1200
KAFGTAAELC VDERMRIASD GIIVVSMEIL RPQPSDTLSE KVIKGKIRIT TRCLWLDKGK  1260
LLDALHKAAH AALSSCPVNC PLHHIERTVS EVLRKLVRKY SSKRPEVIAI AIENPVSVLA  1320
DEINGKLSGK SHVGSGISVL RKAINGDQEK RWSNTTQAEE DNVPEHLMNI AYEEEKGTDI  1380
DIERDTSGEE TTSSSLLQDC SNNDLPSDDF WKPFVTSSTI HPSEENGDGD GSLLQEQLHD  1440
SSVKGNNILF SDVSKSKLKS SKSMTRNKWK PEEVKKLIKM RGELNSKFQV LKGRMALWQE  1500
ISSNLLSDGV SRSPGQCKSL WASLVQKYEE SKKDRKSQEK WPYFKDMDNI LSDLEAPASK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5a0t_A	2e-79	727	1313	19	560	RIBONUCLEASE J
5a0t_B	2e-79	727	1313	19	560	RIBONUCLEASE J
5a0v_A	2e-79	727	1313	19	560	RIBONUCLEASE J
5a0v_B	2e-79	727	1313	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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_019175500.1	0.0	PREDICTED: uncharacterized protein LOC109170789 isoform X3
Swissprot	Q84W56	0.0	RNJ_ARATH; Ribonuclease J
TrEMBL	A0A328D840	0.0	A0A328D840_9ASTE; Uncharacterized protein
STRING	XP_009774848.1	0.0	(Nicotiana sylvestris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA5874	23	31

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]