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

XP_010107394.1

Organism

Morus notabilis

Taxonomic ID

981085

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Moraceae; Morus

Family

LBD

Protein Properties

Length: 614aa MW: 71061 Da PI: 10.202

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_010107394.1	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	124.4	5.5e-39	5	105	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeqpkkfanvhklFGasnvlkllkalpeee.redamsslvyeAearardPvyGavgvilklqqqleqlkael 94 +CaaCk+lrrkC+++C+l+pyfp ++p++fa+vh+++Gasnv+k+l++l+ ++ r +a++sl++eA+ r++dPvyG+v++i++l+qq++++++el XP_010107394.1 5 RCAACKYLRRKCPPECILSPYFPPNDPRRFACVHRIYGASNVVKMLQQLKSHDlRARAANSLYFEAQRRIEDPVYGCVRIITQLHQQIHNAETEL 99 6**********************************************99999*************************************** PP DUF260 95 allkee 100 a++++e XP_010107394.1 100 AKMRAE 105 *99887 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	24.17	4	106	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	2.1E-37	5	103	IPR004883	Lateral organ boundaries, LOB
Gene3D	G3DSA:3.30.70.330	3.1E-18	174	251	IPR012677	Nucleotide-binding alpha-beta plait domain
SuperFamily	SSF54928	3.87E-35	178	346	IPR012677	Nucleotide-binding alpha-beta plait domain
PROSITE profile	PS50102	16.534	178	250	IPR000504	RNA recognition motif domain
CDD	cd12234	5.81E-38	178	249	No hit	No description
SMART	SM00360	4.2E-15	179	246	IPR000504	RNA recognition motif domain
Pfam	PF00076	4.0E-13	180	238	IPR000504	RNA recognition motif domain
Gene3D	G3DSA:3.30.70.330	2.1E-21	263	347	IPR012677	Nucleotide-binding alpha-beta plait domain
PROSITE profile	PS50102	16.227	271	342	IPR000504	RNA recognition motif domain
CDD	cd12466	1.20E-38	272	341	No hit	No description
SMART	SM00360	6.1E-19	272	338	IPR000504	RNA recognition motif domain
Pfam	PF00076	1.3E-14	273	335	IPR000504	RNA recognition motif domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0031053	Biological Process	primary miRNA processing
GO:0010445	Cellular Component	nuclear dicing body
GO:0016607	Cellular Component	nuclear speck
GO:0000166	Molecular Function	nucleotide binding
GO:0003676	Molecular Function	nucleic acid binding

Sequence ? help Back to Top
Protein Sequence Length: 614 aa Download sequence Send to blast
MSPERCAACK YLRRKCPPEC ILSPYFPPND PRRFACVHRI YGASNVVKML QQLKSHDLRA 60 RAANSLYFEA QRRIEDPVYG CVRIITQLHQ QIHNAETELA KMRAEIALKG TTSTATIGHL 120 QGYHHHHHHH YHLYHHHDHH DDQLLEMECD LYSILSQGQS SVDQQSHLIG HATKGKMRPI 180 FCGNFEYDAR QSDLERLFGR YGKVDRVDMK SGFAFIYMED DRDAEDAIRA LDRREFGRKG 240 RRLRVEWTKQ ERGIRRPGGS KKSSANNRPS KTLFVINFDP YHTRTKDLER HFDQYGKIVS 300 VRIRRNFAFV QYESQEDATK ALEATNMSKL MDRVISVEYA VRDDDERKDG YSPDRSRDRS 360 LERGRDRRRS PSPYRRERGS PDYGRGSSPG AYRRERGSPD YGRGRSPSPY KKERASPDYG 420 RGRSPSPYRR ERAGADHGRG SSRSPNRREK VSADRGHGPS HSPYRREKVS ADRGRDRSRS 480 PYGRERGSPD DGRDPSASPY RRRRASPENG RGPSHSPLER ERAEIDNGRE PSPNSVPDPR 540 DSPNYGGPES PMNERYQSMS RKRRHQNEIR LYDKVTMMGS RRTCDYPISI FHVSDHKQQL 600 TPLSALSDTI PLPH

Sequence ? help Back to Top

Protein Sequence Length: 614 aa Download sequence Send to blast

MSPERCAACK YLRRKCPPEC ILSPYFPPND PRRFACVHRI YGASNVVKML QQLKSHDLRA  60
RAANSLYFEA QRRIEDPVYG CVRIITQLHQ QIHNAETELA KMRAEIALKG TTSTATIGHL  120
QGYHHHHHHH YHLYHHHDHH DDQLLEMECD LYSILSQGQS SVDQQSHLIG HATKGKMRPI  180
FCGNFEYDAR QSDLERLFGR YGKVDRVDMK SGFAFIYMED DRDAEDAIRA LDRREFGRKG  240
RRLRVEWTKQ ERGIRRPGGS KKSSANNRPS KTLFVINFDP YHTRTKDLER HFDQYGKIVS  300
VRIRRNFAFV QYESQEDATK ALEATNMSKL MDRVISVEYA VRDDDERKDG YSPDRSRDRS  360
LERGRDRRRS PSPYRRERGS PDYGRGSSPG AYRRERGSPD YGRGRSPSPY KKERASPDYG  420
RGRSPSPYRR ERAGADHGRG SSRSPNRREK VSADRGHGPS HSPYRREKVS ADRGRDRSRS  480
PYGRERGSPD DGRDPSASPY RRRRASPENG RGPSHSPLER ERAEIDNGRE PSPNSVPDPR  540
DSPNYGGPES PMNERYQSMS RKRRHQNEIR LYDKVTMMGS RRTCDYPISI FHVSDHKQQL  600
TPLSALSDTI PLPH

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	5e-30	6	106	12	111	LOB family transfactor Ramosa2.1
5ly0_B	5e-30	6	106	12	111	LOB family transfactor Ramosa2.1
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Functional Description ? help Back to Top
Source	Description
UniProt	Required for constitutive and alternative pre-mRNA splicing (Probable). Involved in primary miRNA processing and pri-miRNA biogenesis. Binds both intronless and intron-containing pri-miRNAs (PubMed:26227967). {ECO:0000269\|PubMed:26227967, ECO:0000305\|PubMed:24146632}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_010107394.1

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_024028642.1	0.0	serine/arginine-rich splicing factor RS40 isoform X1
Swissprot	P92965	1e-116	RS40_ARATH; Serine/arginine-rich splicing factor RS40
TrEMBL	W9S7E2	0.0	W9S7E2_9ROSA; Arginine/serine-rich-splicing factor RSP40
STRING	XP_010107394.1	0.0	(Morus notabilis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF2521	2	2

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G26620.1	5e-45	LOB domain-containing protein 23

Link Out ? help Back to Top
Entrez Gene	21398816

Publications ? help Back to Top
Lorković ZJ,Hilscher J,Barta A Use of fluorescent protein tags to study nuclear organization of the spliceosomal machinery in transiently transformed living plant cells. Mol. Biol. Cell, 2004. 15(7): p. 3233-43 [PMID:15133128] Kalyna M,Barta A A plethora of plant serine/arginine-rich proteins: redundancy or evolution of novel gene functions? Biochem. Soc. Trans., 2004. 32(Pt 4): p. 561-4 [PMID:15270675] Iida K, et al. Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res., 2004. 32(17): p. 5096-103 [PMID:15452276] Gullerova M,Barta A,Lorkovic ZJ AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II. RNA, 2006. 12(4): p. 631-43 [PMID:16497658] Iida K,Go M Survey of conserved alternative splicing events of mRNAs encoding SR proteins in land plants. Mol. Biol. Evol., 2006. 23(5): p. 1085-94 [PMID:16520337] de la Fuente van Bentem S, et al. Phosphoproteomics reveals extensive in vivo phosphorylation of Arabidopsis proteins involved in RNA metabolism. Nucleic Acids Res., 2006. 34(11): p. 3267-78 [PMID:16807317] Kalyna M,Lopato S,Voronin V,Barta A Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins. Nucleic Acids Res., 2006. 34(16): p. 4395-405 [PMID:16936312] Palusa SG,Ali GS,Reddy AS Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses. Plant J., 2007. 49(6): p. 1091-107 [PMID:17319848] Tanabe N,Yoshimura K,Kimura A,Yabuta Y,Shigeoka S Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress. Plant Cell Physiol., 2007. 48(7): p. 1036-49 [PMID:17556373] Barta A,Kalyna M,Reddy AS Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants. Plant Cell, 2010. 22(9): p. 2926-9 [PMID:20884799] Richardson DN, et al. Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing. PLoS ONE, 2011. 6(9): p. e24542 [PMID:21935421] Chen T, et al. A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis. PLoS Genet., 2013. 9(10): p. e1003875 [PMID:24146632] Cruz TM,Carvalho RF,Richardson DN,Duque P Abscisic acid (ABA) regulation of Arabidopsis SR protein gene expression. Int J Mol Sci, 2014. 15(10): p. 17541-64 [PMID:25268622] Chen T,Cui P,Xiong L The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis. Nucleic Acids Res., 2015. 43(17): p. 8283-98 [PMID:26227967] Lopato S,Waigmann E,Barta A Characterization of a novel arginine/serine-rich splicing factor in Arabidopsis. Plant Cell, 1996. 8(12): p. 2255-64 [PMID:8989882]