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

Sof019020

Organism

Saccharum officinarum

Taxonomic ID

4547

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Saccharinae; Saccharum; Saccharum officinarum complex

Family

Trihelix

Protein Properties

Length: 147aa MW: 16640.8 Da PI: 10.2805

Description

Trihelix family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PUT-157a-Saccharum_officinarum-243133727	PU_ref	plantGDB	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	trihelix	61.1	2.7e-19	74	143	1	70
trihelix 1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekk 70 +W+ +e++ Li++r em+e++++ k ++ lWee+s+ m +g++r+p qCk+ w +l ++y++ k+ ++ Sof019020 74 KWKPEEIKSLIQMRGEMNEKFQSVKGRMVLWEEISDTMLNQGISRTPAQCKSLWTSLVQKYEESKKDTES 143 7*************************************************************99987665 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50090	7.863	67	131	IPR017877	Myb-like domain
Gene3D	G3DSA:1.10.10.60	1.2E-6	70	133	IPR009057	Homeodomain-like
SuperFamily	SSF46689	7.34E-5	70	132	IPR009057	Homeodomain-like
Pfam	PF13837	1.6E-14	73	147	No hit	No description
CDD	cd12203	2.34E-20	73	138	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 147 aa Download sequence Send to blast
XTTSSNGEAF FSSDLHQPKT LEHFWESFKS PTAVKIARIV NGGNKQNLGK IGIMGKDSPI 60 QSAPAPVKSS KKNKWKPEEI KSLIQMRGEM NEKFQSVKGR MVLWEEISDT MLNQGISRTP 120 AQCKSLWTSL VQKYEESKKD TESMKTW

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: During the early stages of embryo development, first observed at the transition stage. In the heart and torpedo stages, predominantly present in the upper part of embryos. In seedlings, strongly expressed in shoot meristems, hypocotyls, in the vascular bundles of cotyledons, and in the veins of mature leaves. In reproductive organs, detected in inflorescences, especially in sepals, filaments, and stigmas, as well as in mature siliques and seeds. {ECO:0000269\|PubMed:25871650}.
Uniprot	TISSUE SPECIFICITY: Moslty expressed in inflorescences, seedlings, leaves, flowers and flower buds, and, to a lower extent, in stems, siliques and roots. {ECO:0000269\|PubMed:25871650}.

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_021315489.1	8e-96	uncharacterized protein LOC8079424 isoform X3
Swissprot	Q84W56	4e-30	RNJ_ARATH; Ribonuclease J
TrEMBL	C5XWZ4	5e-93	C5XWZ4_SORBI; Uncharacterized protein
TrEMBL	C5XX00	5e-93	C5XX00_SORBI; Uncharacterized protein
STRING	Sb04g005900.1	9e-94	(Sorghum bicolor)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G63420.1	2e-32	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]