ddG-Matrix: Transcription intiator element, Inr, with single nucleotide substitutions

Input DNA Sequence :
from Screen:

from DB: Bases Available:
from File: File formats here.

Select one either of 27 Inr-dependent or, since YY1 may also bind Inr (see two marks, #'s, below), of 7 additional YY1-dependent models listed below:

(A) Five Inr-activity prediction procedures optimized over the point mutation ddG magnitudes:

SV40 MLP Inr ddG: 50% Lesser ddG increases with Direction
SV40 MLP Inr ddG: 50% Higher ddG increases with Twist (DNA-protein)
SV40 MLP Inr ddG: Transcription in vivo ddG via Direction and Twist (DNA-protein)
SV40 MLP Inr ddG: Additive ddG-matrix Score
SV40 MLP Inr ddG: Multiple mutation ddG via Point mutation ddG

(B) Twelve additional prediction procedures adapted to the others Inr-dependent activities positioned by Transcription Start:
SV40 MLP Inr ddG: Natural high-eukaryota Inr recognition adapted to EPD database
SV40 MLP Inr ddG: Natural primitive T.v. Inr recognition adapted to EMBL Data Library
SV40 MLP Inr ddG: Primitive T.v. Inr transcription, ddG
SV40 MLP Inr ddG: Hybrid {AdML TATA}/{TdT Inr} promotor TFIID-induced, ddG
SV40 MLP Inr ddG: Minimal {Inr+TAF(II)250+TAF(II)150} transcription complex Sp1-induced, ddG
SV40 MLP Inr ddG: Basal {Inr+TAF(II)250+TAF(II)150} transcription, ddG
SV40 MLP Inr ddG: Human hsp70/AdML-hybrid promoter transcription, ddG
SV40 MLP Inr ddG: Human hsp70/AdML-hybrid promoter protection against DNAse I, ddG
SV40 MLP Inr ddG: Hybrid [{weak TATA}+{TdT Inr}] promoter Sp1-induced in vitro, ddG
SV40 MLP Inr ddG: Synthetic Inr-element basal transcription with HeLa cell nuclear extract, ddG
SV40 MLP Inr ddG: Randomly mutated {TdT Inr} basal transcription with HeLa cell nuclear extract, ddG
SV40 MLP Inr ddG: Randomly mutated {TdT Inr} transcription YY1-induced with HeLa cell nuclear extract, ddG, (#)

(C) Ten more prediction procedures adapted to the others Inr-dependent activities delocalized in the neighbourhood of Transcription Start:
SV40 MLP Inr ddG: Natural D.m. TATA-less specific Inr recognition adapted to EMBL Data Library
SV40 MLP Inr ddG: Hybrid [{weak TATA}+{TdT Inr}] promoter Sp1-induction in vivo, Relative
SV40 MLP Inr ddG: Basal TFIID/Inr transcription, ddG
SV40 MLP Inr ddG: TIM (TdT-Inr-protein)/MHC-II-Ea-Inr-element affinity, ddG
SV40 MLP Inr ddG: D-complex (TFIID+TAFs)/MHC-II-Ea Inr-element affinity, ddG
SV40 MLP Inr ddG: DA-complex (TFIID+TAFs+TFIIA)/MHC-II-Ea Inr-element, ddG
SV40 MLP Inr ddG: Basal MHC-II-Ea Inr transcription, ddG
SV40 MLP Inr ddG: LBP-1 (HIV Inr-protein)/MHC-II-Ea Inr-element, ddG
SV40 MLP Inr ddG: {Human MDR1 promoter}+{Inr+gene b-globine}+HeLa, ddG
SV40 MLP Inr ddG: (TdT-like Inr mutant)/YY1-affinity, ddG, (#)

(D) Seven more prediction procedures adapted, since YY1 may also bind Inr (see two marks, #'s, above), to the YY1-dependent activities:
SV40 MLP Inr ddG: {TdT YY1}/{HeLa nuclear extract} affinity, ddG
SV40 MLP Inr ddG: Randomized/selected YY1-affinit-oligoDNA binds transcription factor YY1, ddG
SV40 MLP Inr ddG: LUC-gene reporter-activity YY1-repressed within pTiLUC-plasmid and HeLa cell, ddG
SV40 MLP Inr ddG: LUC-gene reporter-activity YY1-repressed within pGL2-plasmid and HeLa cell, ddG
SV40 MLP Inr ddG: LUC-gene reporter-activity YY1-repressed within pTiLUC-plasmid and PYS-2 cell ddG
SV40 MLP Inr ddG: Natural experimental YY1-sites recognition adapted to TRRD and TRANSFAC databases
SV40 MLP Inr ddG: Randomized/selected YY1-affinit-oligoDNA recognition adapted to SELEX_DB

This resource has been developed in collaboration between
The Institute of Cytology and Genetics (Novosibirsk, Russia) and The Institute of Physical and Chemical Research, RIKEN (Thukuba, Japan)
that was supported by RFBR grant #98-07-90126 (Russia) and STA Fellow #499042 (Japan)

Author: Misha Ponomarenko, Ph.D.
Contributors: Julia Ponomarenko, Ms.D., Galina Orlova, Ph.D., Sergey Lavrushev, Ms.D., Anatoly Frolov, Ph.D.
Supervisors: Nikolay Kolchanov, Prof. and Akinori Sarai, Prof.