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Matrix Family Library Version 6.3

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

Matrix Family Library Version 6.3 (March 2007) contains 737 weight matrices in 301 families classified into the following groups:

The vertebrate group represents binding site descriptions of 3113 transcription factors: The plant group represents binding site descriptions of 573 transcription factors from several plant species.


New weight matrices

Vertebrates

Family Family Information Matrix Name Matrix Information
V$HOMF Homeodomain transcription factors V$NOBOX.01 Homeobox containing germ cell-specific transcription factor NOBOX
V$NR2F Nuclear receptor subfamily 2 factors V$HNF4.03 Hepatic nuclear factor 4, DR1 sites
V$TR2_TR4.01 DR1 binding sites for TR2 homodimers or TR2/TR4 heterodimers
V$TR4.01 TR4 homodimer, DR1 site
V$P53F p53 tumor suppressor V$P53.04 Tumor suppressor p53
V$P53.05 Tumor suppressor p53
V$P53.06 Tumor suppressor p53
V$PAX6 PAX-4/PAX-6 paired domain binding sites V$PAX6.03 PAX6 paired domain binding site
V$PAX6.04 PAX6 paired domain binding site
V$RORA v-ERB and RAR-related orphan receptor alpha V$REV-ERBA.01 Orphan nuclear receptor rev-erb alpha (NR1D1)
V$REV-ERBA.02 Orphan nuclear receptor rev-erb alpha (NR1D1), homodimer DR2 binding site
V$REV-ERBA.03 Orphan nuclear receptor rev-erb alpha (NR1D1), homodimer DR2 binding site
V$RORA.01 RAR-related orphan receptor alpha
V$RORGAMMA.01 RAR-related orphan receptor gamma
V$RXRF RXR heterodimer binding sites V$CAR_RXR.01 Constitutive androstane receptor / retinoid X receptor heterodimer, DR4 sites
V$PXR_RXR.01 Pregnane X receptor / retinoid X receptor heterodimer, DR4 sites
V$RAR_RXR.01 Retinoic acid receptor / retinoid X receptor heterodimer, DR1 sites
V$RAR_RXR.02 Retinoic acid receptor / retinoid X receptor heterodimer, DR2 sites
V$RAR_RXR.03 Retinoic acid receptor / retinoid X receptor heterodimer, DR5 sites
V$RXR_RXR.01 Retinoid X receptor homodimer, DR1 sites
V$THR.01 THR/RXR heterodimer and THR homodimer DR4 binding sites


Plants

Family Family Information Matrix Name Matrix Information
P$CE1F Coupling element 1 binding factors P$SBOX.01 Sugar and ABA responsive element conserved in several rbcS promoters
P$IDRE Iron-deficiency response elements P$IDE1.01 Iron-deficiency-responsive element 1
P$MYCL Myc-like basic helix-loop-helix binding factors P$OSIRO2.01 Rice iron-related transcription factor 2
P$PREM Motifs of plastid response elements P$MGPROTORE.01 Promoter elements involved in MgProto (Mg-protoporphyrin IX) and light-mediated induction
P$SBPD SBP-domain proteins P$SBP.01 SQUA promoter binding proteins
P$SURE Sugar response elements, SURE and SURE-like sequences in plant promoters P$SURE.01 Sugar responsive elements



Weight matrices moved to other families


Weight matrices renamed

The following weight matrices have been renamed because of the previously incorrect naming:

Weight matrices modified

The following weight matrices have been replaced by better matrices:

Weight matrices removed

The following weight matrices have been removed because they describe only half sites to which the corresponding transcription factors do not bind: