Genomatix-Logo
Overview of Help-Pages
GEMS Launcher Logo

Matrix Family Library Version 4.0

[New weight matrices] [Weight matrices modified]
[Weight matrices moved to other families] [Matrix families renamed]
[Changes in previous release] [View all matrices]


Matrix Family Library Version 4.0 (November 2003) contains 535 weight matrices in 253 families classified into the following groups:

New weight matrices

Vertebrates

Family Family Information Matrix Name Matrix Information
V$AARF AARE binding factors V$AARE.01 Amino acid response element, ATF4 binding site
V$AP1R MAF and AP1 related factors V$BACH2.01 Bach2 bound TRE
V$NFE2L2.01 Nuclear factor (erythroid-derived 2)-like 2, NRF2
V$CDXF Vertebrate caudal related homeodomain protein V$CDX1.01 Intestine specific homeodomain factor CDX-1
V$DEAF Homolog to deformed epidermal autoregulatory factor-1 from D. melanogaster V$NUDR.01 NUDR (nuclear DEAF-1 related transcriptional regulator protein
V$ETSF Human and murine ETS1 factors V$ELF2.01 Ets - family member ELF-2 (NERF1a)
V$GABF GA-boxes V$GAGA.01 GAGA-Box
V$HNF1 Hepatic Nuclear Factor 1 V$HNF1.03 Hepatic nuclear factor 1
V$HOXF Factors with moderate activity to homeo domain consensus sequence V$GSC.01 Vertebrate bicoid-type homeodomain protein Goosecoid
V$LHXF Lim homeodomain factors V$LHX3.01 Homeodomain binding site in LIM/Homeodomain factor LHX3
V$NKXH NKX/DLX - homeodomain sites V$NKX32.01 Homeodomain protein NKX3.2 (BAPX1, NKX3B, Bagpipe homolog)
V$RBPF RBPJ - kappa V$RBPJK.02 Mammalian transcriptional repressor RBP-Jkappa/CBF1
V$RP58 RP58 (ZFP238) zinc finger protein V$RP58.01 Zinc finger protein RP58 (ZNF238), associated preferentially with heterochromatin


Plants

Family Family Information Matrix Name Matrix Information
P$ABRE ABA response elements P$ABRE.01 ABA response elements
P$AGLF Agamous like factors P$AGL1.01 AGL1, Arabidopsis MADS-domain protein AGAMOUS-like 1
P$AGL2.01 AGL2, Arabidopsis MADS-domain protein AGAMOUS-like 2
P$AGL15.01 AGL15, Arabidopsis MADS-domain protein AGAMOUS-like 15
P$AHBP Arabidopsis homeobox protein P$ATHB9.01 HD-ZIP class III protein ATHB9
P$AREF Auxin response element P$SEBF.01 Silencing element binding factor - transcriptional repressor
P$BZIP Plant G-box/C-box BZIP Proteins P$HBP1B.01 Wheat bZIP transcription factor HBP1B (histone gene binding protein 1b)
P$UPRE.01 UPRE (unfolded protein response element) like motif
P$CAAT CCAAT binding factors P$CAAT.01 CCAAT-box in plant promoters
P$CAAT.02 CCAAT-box in plant promoters
P$DPBF Dc3 promoter binding factors P$DPBF.01 bZIP factors DPBF-1 and 2 (Dc3 promoter binding factor-1 and 2)
P$ERSE ER stress-response elements P$ERSE_I.01 ERSE I (ER stress-response element I)-like motif
P$GAGA GAGA elements P$GAGABP.01 (GA)n/(CT)n binding proteins (GBP, soybean; BBR, barley)
P$GTBX GT-box elements P$GT1.01 GT1-Box binding factors with a trihelix DNA-binding domain
P$SF1.01 S1F, site 1 binding factor of spinach rps1 promoter
P$IBOX Plant I-Box sites P$GATA.01 Class I GATA factors
P$LEGB Legumin Box family P$RY.01 RY and Sph motifs conserved in seed-specific promoters
P$MIIG MYB IIG-type binding sites P$ATMYB15.01 R2R3-type myb-like transcription factor (IIG-type binding site)
P$ATMYB84.01 R2R3-type myb-like transcription factor (IIG-type binding site)
P$PALBOXL.01 Cis-acting element conserved in various PAL and 4CL promoters
P$PALBOXP.01 Putative cis-acting element in various PAL and 4CL gene promoters
P$MYBL MYB-like proteins P$ATMYB77.01 R2R3-type myb-like transcription factor (I-type binding site)
P$MYBS MYB proteins with single DNA binding domains P$OSMYBS.01 Rice MYB proteins with single DNA binding domains, binding to the amylase element (TATCCA)
P$OCSE Enhancer element first identified in the promoter of the octopine synthase gene (OCS) of the Agrobacterium tumefaciens T-DNA P$OCSTF.01 bZIP transcription factor binding to OCS-elements
P$PALA Conserved box A in PAL and 4CL gene promoters P$PALBOXA.01 Putative cis-acting element on various PAL and 4CL gene promoters
P$PALB PAL-box P$NTLIM1.01 LIM domain protein binding to a PAL-box like sequence
P$PSRE Pollen-specific regulatory elements P$GAAA.01 GAAA motif involved in pollen specific transcriptional activation
P$SALT Salt/drought responsive elements P$ALFIN1.02 Zinc-finger protein in alfalfa roots, regulates salt tolerance
P$SEF Soybean embryo factor 3 P$SEF3.01 SEF3, Soybean embryo factor 3
P$TALE TALE (3-aa acid loop extension) class homeodomain proteins P$HVH21.01 Homeodomain protein of the Knotted class1
P$TBPF TATA binding protein factor P$TATA.01 Plant TATA box
P$TATA.02 Plant TATA box
P$TEFB TEF-box P$TEF1.01 TEF cis acting elements in both RNA polymerase II-dependent promoters and rDNA spacer sequences
P$WBXF W Box family P$ERE.01 Elicitor response element


Insects

Family Family Information Matrix Name Matrix Information
I$DPCG Cis-acting silencer sequences binding Drosophila polycomp group proteins I$PHO.01 PHO (pleiohomeotic) and PHO-like, polycomp group proteins (PcG) binding to PREs (polycomb group response elements)
I$GAGA GAGA element, binding sites for proteins of the trithorax group (trxG) I$GAF.01 GAGA factor encoded by the Trithorax-like gene (Trl)


Fungi

Family Family Information Matrix Name Matrix Information
F$MREF Metal regulatory element factors F$CUSE.01 Copper-signaling element, AMT1/ACE1 recognition sequence


Weight matrices modified

The following weight matrices have been replaced by better matrices:


Weight matrices moved to other families


Matrix families renamed