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.004G178300.2.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

C3H

Protein Properties

Length: 768aa MW: 87448.5 Da PI: 8.4448

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.004G178300.2.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	22.8	1.6e-07	230	249	6	25
-SGGGGTS--TTTTT-SS-S CS zf-CCCH 6 CrffartGtCkyGdrCkFaH 25 C+f+++tG C++G rC++ H Sobic.004G178300.2.p 230 CPFHLKTGACRFGVRCSRVH 249 ******************99 PP
2	zf-CCCH	24.1	6.2e-08	378	405	1	26
--S---SGGGGTS..--TTTTT-SS-SS CS zf-CCCH 1 yktelCrffartG..tCkyGdrCkFaHg 26 +k ++C +++r+ tC++G C+F+H+ Sobic.004G178300.2.p 378 WKAAICGDYMRSRykTCSHGVACNFIHC 405 7889***********************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	11.807	224	252	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2	225	251	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.9E-5	229	249	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	4.9E-34	230	249	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	4.9E-34	249	269	IPR009145	U2 auxiliary factor small subunit
Gene3D	G3DSA:3.30.70.330	2.1E-24	256	373	IPR012677	Nucleotide-binding alpha-beta plait domain
CDD	cd12540	1.41E-45	257	373	No hit	No description
PROSITE profile	PS50102	9.712	287	375	IPR000504	RNA recognition motif domain
SMART	SM00361	6.3E-8	295	371	IPR003954	RNA recognition motif domain, eukaryote
PRINTS	PR01848	4.9E-34	300	315	IPR009145	U2 auxiliary factor small subunit
SuperFamily	SSF54928	2.17E-17	306	374	IPR012677	Nucleotide-binding alpha-beta plait domain
Pfam	PF00076	1.9E-4	312	368	IPR000504	RNA recognition motif domain
PRINTS	PR01848	4.9E-34	332	354	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	4.9E-34	359	383	IPR009145	U2 auxiliary factor small subunit
SMART	SM00356	0.044	377	406	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	10.662	377	407	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.3E-5	378	405	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	4.9E-34	397	409	IPR009145	U2 auxiliary factor small subunit

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000398	Biological Process	mRNA splicing, via spliceosome
GO:0089701	Cellular Component	U2AF
GO:0000166	Molecular Function	nucleotide binding
GO:0003723	Molecular Function	RNA binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 768 aa Download sequence Send to blast
MSSAVTAGGG AAAADGAPEA AATALTRREK RRERKKERRR RARREAAARA RAAAEAEAPA 60 ATDPEEERRL LEIQEAEAAA ESERARLAFE DAERRWLEAA AARAAEKAAA AAAEEEARAA 120 EASARKEPKD DQGNQSEEDS EWEYVEDGPA EIIWKGNEII VKKKKVKVPK GSKEKLPVQE 180 EDRPTSNPLP PQSVAFAAQR REPSLSAQEV LDKVAQETPN FGTEQDKAHC PFHLKTGACR 240 FGVRCSRVHF YPDKSSTLLM KNMYNGPGLA LDQDEGLEIA CSFVLSSELR LEAYSDQFTD 300 EEIEQSYEEF YEDVHTEFLK FGELVNFKVC RNGCFHLRGN VYVHYKSLDS ALLAYSSMNG 360 RYFAGKQITC EFVAVTRWKA AICGDYMRSR YKTCSHGVAC NFIHCFRNPG GDYEWADWDN 420 PPPRYWIRKM TALFGPSVDT MYEKESDTPN FKSSEGSDRK KLKISSNRYV SRGSRDEDVH 480 TRHSQDYSHS KQEHSSHSMN YEYKRHRRDS SSVDKHRRRD VEDTNGRQFS TMENDSESHR 540 HKHEERHRSD HGNGEKKDDK TRPRKHCSDR RGSLEPGYSD WPSDFTDTDI RKGSSGEKST 600 SRYEYDDAKR SRRGSSEYYN LERHHSTAQK PTGKEHNTKR RSRRDIEDYY HDEKDGGRGK 660 SRKHDRWVAT NSDVDSDVDR YQSSSCKGTR SGRKEDAHPD SEAWHQRSSR STKDDRRRKR 720 HSGTEEGTSE SSSGDLSSDS GSRRSRSSEN FSAHRSKRKR SVGKKSS*

Sequence ? help Back to Top

Protein Sequence Length: 768 aa Download sequence Send to blast

MSSAVTAGGG AAAADGAPEA AATALTRREK RRERKKERRR RARREAAARA RAAAEAEAPA  60
ATDPEEERRL LEIQEAEAAA ESERARLAFE DAERRWLEAA AARAAEKAAA AAAEEEARAA  120
EASARKEPKD DQGNQSEEDS EWEYVEDGPA EIIWKGNEII VKKKKVKVPK GSKEKLPVQE  180
EDRPTSNPLP PQSVAFAAQR REPSLSAQEV LDKVAQETPN FGTEQDKAHC PFHLKTGACR  240
FGVRCSRVHF YPDKSSTLLM KNMYNGPGLA LDQDEGLEIA CSFVLSSELR LEAYSDQFTD  300
EEIEQSYEEF YEDVHTEFLK FGELVNFKVC RNGCFHLRGN VYVHYKSLDS ALLAYSSMNG  360
RYFAGKQITC EFVAVTRWKA AICGDYMRSR YKTCSHGVAC NFIHCFRNPG GDYEWADWDN  420
PPPRYWIRKM TALFGPSVDT MYEKESDTPN FKSSEGSDRK KLKISSNRYV SRGSRDEDVH  480
TRHSQDYSHS KQEHSSHSMN YEYKRHRRDS SSVDKHRRRD VEDTNGRQFS TMENDSESHR  540
HKHEERHRSD HGNGEKKDDK TRPRKHCSDR RGSLEPGYSD WPSDFTDTDI RKGSSGEKST  600
SRYEYDDAKR SRRGSSEYYN LERHHSTAQK PTGKEHNTKR RSRRDIEDYY HDEKDGGRGK  660
SRKHDRWVAT NSDVDSDVDR YQSSSCKGTR SGRKEDAHPD SEAWHQRSSR STKDDRRRKR  720
HSGTEEGTSE SSSGDLSSDS GSRRSRSSEN FSAHRSKRKR SVGKKSS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4yh8_A	4e-29	221	404	9	167	Splicing factor U2AF 23 kDa subunit
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	30	38	RRERKKERR
2	37	44	RRRRARRE

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.004G178300.2.p

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	JN791418	0.0	JN791418.1 Zea mays rough endosperm 3-umu1 gamma isoform (Rgh3) mRNA, Rgh3-umu1 allele, complete cds, alternatively spliced.
GenBank	JN791423	0.0	JN791423.1 Zea mays rough endosperm 3 beta isoform 4 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBank	JN791427	0.0	JN791427.1 Zea mays rough endosperm 3 gamma isoform 4 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBank	JN791429	0.0	JN791429.1 Zea mays rough endosperm 3 gamma isoform 6 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBank	JN791430	0.0	JN791430.1 Zea mays rough endosperm 3 gamma isoform 7 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBank	JN791433	0.0	JN791433.1 Zea mays rough endosperm 3 delta isoform (Rgh3) mRNA, complete cds, alternatively spliced.
GenBank	JN791435	0.0	JN791435.1 Zea mays rough endosperm 3 eta isoform (Rgh3) mRNA, complete cds, alternatively spliced.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021314210.1	0.0	zinc finger CCCH domain-containing protein 16 isoform X1
Swissprot	Q6YVX9	0.0	C3H16_ORYSJ; Zinc finger CCCH domain-containing protein 16
TrEMBL	A0A1Z5RN03	0.0	A0A1Z5RN03_SORBI; Uncharacterized protein
STRING	Sb04g022810.1	0.0	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP9296	13	17
Representative plant	OGRP5926	6	6

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G44785.1	3e-11	C3H family protein

Link Out ? help Back to Top
Phytozome	Sobic.004G178300.2.p

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764]