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

Sobic.004G070400.1.p

Organism

Sorghum bicolor

Taxonomic ID

4558

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum

Family

Trihelix

Protein Properties

Length: 404aa MW: 44720 Da PI: 8.7824

Description

Trihelix family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.004G070400.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	trihelix	57.1	4.9e-18	334	395	1	62
trihelix 1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkryk 62 +W+ +e++ Li++r em+e++++ k ++ lWee+s+ m +g++r+p qCk+ w +l ++y+ Sobic.004G070400.1.p 334 KWKPEEIKSLIQMRGEMNEKFQSVKGRMVLWEEISDTMLNQGISRTPAQCKSLWTSLVQKYE 395 7***********************************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50090	7.863	327	391	IPR017877	Myb-like domain
Gene3D	G3DSA:1.10.10.60	8.5E-6	330	393	IPR009057	Homeodomain-like
Pfam	PF13837	6.1E-13	333	395	No hit	No description
CDD	cd12203	1.01E-21	333	395	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: 404 aa Download sequence Send to blast
EEVLHIVKPQ HFLPVHGELL FLKEHELLGR STGIRHTTVS NKNGEVLGVS HLRNRRVLSN 60 GFVSLGKEDL QLMYSDGDKA FGTSTDLCID ERLRIASDGI IFVSMEIFRP QKEHGLAQSG 120 LKGKFKITTI CLWLDNGRLL DALYKAAHAA LSSCPVNCPL SHMERMVAEI LRKMVRKYSG 180 KKPDVIAVAT ENSMAGFSEH LDAKSSGNFG PSSATSHLSR SPATSLEGSY KTHPDNPEVD 240 AEVLCHTETP PEAVRTTPDD ATTSSNGEAF FSSDLHQPKT LEHFWESFKS PTAVKIARIV 300 NGGNKQNLSK IGIMGKDSSI QSAPAPVKSS KKNKWKPEEI KSLIQMRGEM NEKFQSVKGR 360 MVLWEEISDT MLNQGISRTP AQCKSLWTSL VQKYEVSHRF SFF*

Sequence ? help Back to Top

Protein Sequence Length: 404 aa Download sequence Send to blast

EEVLHIVKPQ HFLPVHGELL FLKEHELLGR STGIRHTTVS NKNGEVLGVS HLRNRRVLSN  60
GFVSLGKEDL QLMYSDGDKA FGTSTDLCID ERLRIASDGI IFVSMEIFRP QKEHGLAQSG  120
LKGKFKITTI CLWLDNGRLL DALYKAAHAA LSSCPVNCPL SHMERMVAEI LRKMVRKYSG  180
KKPDVIAVAT ENSMAGFSEH LDAKSSGNFG PSSATSHLSR SPATSLEGSY KTHPDNPEVD  240
AEVLCHTETP PEAVRTTPDD ATTSSNGEAF FSSDLHQPKT LEHFWESFKS PTAVKIARIV  300
NGGNKQNLSK IGIMGKDSSI QSAPAPVKSS KKNKWKPEEI KSLIQMRGEM NEKFQSVKGR  360
MVLWEEISDT MLNQGISRTP AQCKSLWTSL VQKYEVSHRF SFF*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Sbi.18736	0.0	leaf

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.004G070400.1.p

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	EU952205	0.0	EU952205.1 Zea mays clone 1223255 hypothetical protein mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021315489.1	0.0	uncharacterized protein LOC8079424 isoform X3
Swissprot	Q84W56	1e-133	RNJ_ARATH; Ribonuclease J
TrEMBL	A0A1Z5RLA5	0.0	A0A1Z5RLA5_SORBI; Uncharacterized protein (Fragment)
STRING	Sb04g005900.1	0.0	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP4996	35	42
Representative plant	OGRP3082	15	21

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G63420.1	1e-136	Trihelix family protein

Link Out ? help Back to Top
Phytozome	Sobic.004G070400.1.p

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]