CIS-BP Database: Catalog of Inferred Sequence Binding Preferences

TF Information

Rfx3 *(Dipodomys ordii)* RFX
Pfam ID	Interpro ID	Gene ID	CIS-BP ID	Sequence source	Animal TF db
PF02257 (RFX_DNA_binding)	IPR003150	ENSDORG00000013906	T318208_2.00	Ensembl (2018-Dec-8)	Link out
Directly determined binding motifs
Name/Motif ID	Species	Forward	Reverse	Type/Study/Study ID	SR Score	DBD Identity
No direct experiments
Motifs from related TFs
Name/Motif ID	Species	Forward	Reverse	Type/Study/Study ID	SR Score	DBD Identity
RFX3 M03452_2.00	Homo sapiens	NGTTRCCATGGHAACV	BGTTDCCATGGYAACN	SELEX Jolma et al.(2013) RFX3_1	0.779	1.000
RFX3 M03453_2.00	Homo sapiens	BGTTGCTARGCAACS	SGTTGCYTAGCAACV	SELEX Jolma et al.(2013) RFX3_2	0.779	1.000
RFX3 M02750_2.00	Homo sapiens	GTTRYYATGG	CCATRRYAAC	SELEX Jolma et al.(2010) RFX3_dimer	0.779	1.000
RFX3 M05715_2.00	Homo sapiens	NGTTRYYATRRYAACN	NGTTRYYATRRYAACN	SELEX Yin et al.(2017) RFX3_eDBD_HT-SELEX_1	0.779	1.000
RFX3 M05716_2.00	Homo sapiens	BGTTGCTARGCAACS	SGTTGCYTAGCAACV	SELEX Yin et al.(2017) RFX3_eDBD_HT-SELEX_2	0.779	1.000
RFX3 M09361_2.00	Homo sapiens	BGTTRCCATGGYRN	NYRCCATGGYAACV	Misc Kulakovskiy et al.(2013) RFX3_HUMAN.H11MO.0.B	0.779	1.000
RFX3 M09627_2.00	Homo sapiens	BNGTTGCCATGGCAAC	GTTGCCATGGCAACNV	Misc Heinz et al.(2010) K562-RFX3_SRA012198	0.779	1.000
RFX3 M05717_2.00	Homo sapiens	BGTTRYYATRRYAACV	BGTTRYYATRRYAACV	SELEX Yin et al.(2017) RFX3_eDBD_Methyl-HT-SELEX_1	0.779	1.000
RFX3 M05718_2.00	Homo sapiens	BGTTGCTARGCAACV	BGTTGCYTAGCAACV	SELEX Yin et al.(2017) RFX3_eDBD_Methyl-HT-SELEX_2	0.779	1.000
RFX2 M03454_2.00	Homo sapiens	BGTTRCCATGGYAACV	BGTTRCCATGGYAACV	SELEX Jolma et al.(2013) RFX2_1	0.775	0.962
RFX2 M03455_2.00	Homo sapiens	SGTTGCTARGCAACS	SGTTGCYTAGCAACS	SELEX Jolma et al.(2013) RFX2_2	0.775	0.962
RFX2 M05719_2.00	Homo sapiens	NGTWDYYATRRHWACN	NGTWDYYATRRHWACN	SELEX Yin et al.(2017) RFX2_eDBD_HT-SELEX	0.775	0.962
RFX2 M09362_2.00	Homo sapiens	YNGTTGCCATGGVRACVV	BBGTYBCCATGGCAACNR	Misc Kulakovskiy et al.(2013) RFX2_HUMAN.H11MO.0.A	0.775	0.962
RFX2 M09628_2.00	Homo sapiens	BGTTKCCATGGMAAC	GTTKCCATGGMAACV	Misc Heinz et al.(2010) LoVo-RFX2_GSE49402	0.775	0.962
RFX2 M05720_2.00	Homo sapiens	BGTTRCCATGRYAACV	BGTTRYCATGGYAACV	SELEX Yin et al.(2017) RFX2_eDBD_Methyl-HT-SELEX	0.775	0.962
Rfx2 M03461_2.00	Mus musculus	BGTTRCCATGGYAACV	BGTTRCCATGGYAACV	SELEX Jolma et al.(2013) Rfx2_1	0.773	0.949
Rfx2 M03462_2.00	Mus musculus	SGTTGCTARGCAACV	BGTTGCYTAGCAACS	SELEX Jolma et al.(2013) Rfx2_2	0.773	0.949
Rfx2 M05888_2.00	Mus musculus	NGTTRCYATGGHDAY	RTHDCCATRGYAACN	SMiLE-seq Isakova et al.(2017) RFX2	0.773	0.949
Rfx2 M09366_2.00	Mus musculus	NBYBGTYNCCMTGGCAACNSSS	SSSNGTTGCCAKGGNRACVRVN	Misc Kulakovskiy et al.(2013) RFX2_MOUSE.H11MO.0.A	0.773	0.949
Rfx3 M00188_2.00	Mus musculus	SNTRRHDACN	NGTHDYYANS	PBM Badis et al.(2009) Rfx3_3961	0.768	0.962
Rfx3 M03463_2.00	Mus musculus	SGTTRCCATGGYAACS	SGTTRCCATGGYAACS	SELEX Jolma et al.(2013) Rfx3_1	0.768	0.962
Rfx3 M09368_2.00	Mus musculus	BBGTTGCCATGGNRAC	GTYNCCATGGCAACVV	Misc Kulakovskiy et al.(2013) RFX3_MOUSE.H11MO.0.C	0.768	0.962
RFX2 M02449_2.00	Homo sapiens	BGTHRYYADG	CHTRRYDACV	PBM Weirauch et al.(2014) pTH9194	0.764	0.923
RFX2 M02450_2.00	Ornithorhynchus anatinus	NGTHRYYANV	BNTRRYDACN	PBM Weirauch et al.(2014) pTH9269	0.764	0.923
RFX1 M02447_2.00	Anolis carolinensis	GTHRCYANGN	NCNTRGYDAC	PBM Weirauch et al.(2014) pTH9223	0.762	0.846
RFX1 M02451_2.00	Tetraodon nigroviridis	GTHDYYANGN	NCNTRRHDAC	PBM Weirauch et al.(2014) pTH9385	0.762	0.846
RFX1 M05723_2.00	Homo sapiens	BGTTRYCATGRYAACV	BGTTRYCATGRYAACV	SELEX Yin et al.(2017) RFX1_eDBD_HT-SELEX	0.762	0.846
Rfx1 M08162_2.00	Mus musculus	GTTGCYADGGNRAC	GTYNCCHTRGCAAC	ChIP-seq Mathelier et al.(2014) MA0509.1	0.762	0.846
RFX1 M09363_2.00	Homo sapiens	BBBSSNGTTGCCADGGNRMCVV	BBGKYNCCHTGGCAACNSSVVV	Misc Kulakovskiy et al.(2013) RFX1_HUMAN.H11MO.0.B	0.762	0.846
Rfx1 M09367_2.00	Mus musculus	BBBSSNGTTGCCADGGNRMCVV	BBGKYNCCHTGGCAACNSSVVV	Misc Kulakovskiy et al.(2013) RFX1_MOUSE.H11MO.0.A	0.762	0.846
RFX1 M11245_2.00	Homo sapiens	Transfac license required	Transfac license required	Transfac Matys et al.(2006) V$EFC_Q6	0.762	0.846
RFX1 M11246_2.00	Homo sapiens	HNGTTRCYWVGYDMYNN	NNRKHRCBWRGYAACND	Transfac Matys et al.(2006) V$RFX1_01	0.762	0.846
RFX1 M11247_2.00	Homo sapiens	HNGTTRCYWBVGYDMYNN	NNRKHRCBVWRGYAACND	Transfac Matys et al.(2006) V$RFX1_02	0.762	0.846
RFX1 M11248_2.00	Homo sapiens	Transfac license required	Transfac license required	Transfac Matys et al.(2006) V$RFX1_Q6	0.762	0.846
RFX1 M05724_2.00	Homo sapiens	BGTWRYCATGRYWACV	BGTWRYCATGRYWACV	SELEX Yin et al.(2017) RFX1_eDBD_Methyl-HT-SELEX	0.762	0.846
GB41876 M02453_2.00	Apis mellifera	GTHDCYANVN	NBNTRGHDAC	PBM Weirauch et al.(2014) pTH9226	0.760	0.859
XP_002157607.1 M02456_2.00	Hydra magnipapillata	GTHDYYDNVN	NBNHRRHDAC	PBM Weirauch et al.(2014) pTH9199	0.757	0.808
G4VLF2_SCHMA M02452_2.00	Schistosoma mansoni	GTTGCTAD	HTAGCAAC	PBM Weirauch et al.(2014) pTH8587	0.756	0.821
Sjc_0102030 M02455_2.00	Schistosoma japonicum	GTTRCYANG	CNTRGYAAC	PBM Weirauch et al.(2014) pTH9285	0.755	0.808
Rfx M03959_2.00	Drosophila melanogaster	NGTHRCYATRGYDACN	NGTHRCYATRGYDACN	SELEX Nitta et al.(2015) Rfx_1	0.751	0.808
Rfx M03960_2.00	Drosophila melanogaster	GTTGCTARGCAAC	GTTGCYTAGCAAC	SELEX Nitta et al.(2015) Rfx_2	0.751	0.808
Rfx M03961_2.00	Drosophila melanogaster	BGTWRCCATGGYWACV	BGTWRCCATGGYWACV	SELEX Nitta et al.(2015) Rfx_3	0.751	0.808
Rfx M03962_2.00	Drosophila melanogaster	GTTRCYAWTRGYAAC	GTTRCYAWTRGYAAC	SELEX Nitta et al.(2015) Rfx_4	0.751	0.808
Rfx M03963_2.00	Drosophila melanogaster	GTTGCTARGCAAC	GTTGCYTAGCAAC	SELEX Nitta et al.(2015) Rfx_5	0.751	0.808
PHUM046580 M02454_2.00	Pediculus humanus	NGTHDCYANV	BNTRGHDACN	PBM Weirauch et al.(2014) pTH9278	0.742	0.833
daf-19 M00709_2.00	Caenorhabditis elegans	SGTTRCTADG	CHTAGYAACS	PBM Narasimhan et al.(2015) pTH10021	0.729	0.679
RFX4 M02448_2.00	Cavia porcellus	GTHDYYNNGN	NCNNRRHDAC	PBM Weirauch et al.(2014) pTH9249	0.704	0.654
Rfx4 M00186_2.00	Mus musculus	GTHDYYNNSN	NSNNRRHDAC	PBM Badis et al.(2009) Rfx4_3761	0.704	0.654
RFX4 M03456_2.00	Homo sapiens	NGTWRYCATRGHWACN	NGTWDCYATGRYWACN	SELEX Jolma et al.(2013) RFX4_1	0.704	0.654
RFX4 M03457_2.00	Homo sapiens	NGTTGCYRRGCAACS	SGTTGCYYRGCAACN	SELEX Jolma et al.(2013) RFX4_2	0.704	0.654
RFX4 M05721_2.00	Homo sapiens	BGTWRYCATGRYWACV	BGTWRYCATGRYWACV	SELEX Yin et al.(2017) RFX4_eDBD_HT-SELEX	0.704	0.654
RFX4 M05722_2.00	Homo sapiens	BGTWRYCATGRYWACV	BGTWRYCATGRYWACV	SELEX Yin et al.(2017) RFX4_eDBD_Methyl-HT-SELEX	0.704	0.654
Rfx6 M09365_2.00	Mus musculus	BDGTWKCYNDG	CHNRGMAACHV	Misc Kulakovskiy et al.(2013) RFX6_MOUSE.H11MO.0.C	0.684	0.615
RFX1 M00066_2.00	Saccharomyces cerevisiae	NSGTTGCYAN	NTRGCAACSN	PBM Badis et al.(2008) RFX1_4537	0.651	0.410
RFX1 M07494_2.00	Saccharomyces cerevisiae	BGTTRCYA	TRGYAACV	PBM, CSA and or DIP-chip Mathelier et al.(2014) MA0365.1	0.651	0.410
RFX1 M08600_2.00	Saccharomyces cerevisiae	CGTYRBYAYRGYWACM	KGTWRCYRTRVYRACG	Misc DeBoer et al.(2011) YLR176C_1478	0.651	0.410
RFX1 M08601_2.00	Saccharomyces cerevisiae	BGTTRCYA	TRGYAACV	Misc DeBoer et al.(2011) YLR176C_496	0.651	0.410
RFX1 M11251_2.00	Saccharomyces cerevisiae	Transfac license required	Transfac license required	Transfac Matys et al.(2006) F$RFX1_02	0.651	0.410
For this family, TFs with SR scores > 0.650* will likely have a similar motif*

DNA Binding Domains

Protein ID	Domain	From	To	Sequence
ENSDORP00000013072	RFX	181	258	NSHLQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKLDPVNAASFGKLIRSIFMGLRTRRLGTRGNSKYHYYGIRVKP

Links
Other RFX family TFs
Other *Dipodomys ordii* TFs

693 Related TFs

Name	Species	Gene ID	Motif Evidence	SR Score	Action
AALB006731	Anopheles albimanus	AALB006731	N
Aan_R006597	Calypte anna	Aan_R006597	N
AFAF008476	Anopheles farauti	AFAF008476	N
Afo_R014607	Aptenodytes forsteri	Afo_R014607	N
ALUE_0001723701	Ascaris lumbricoides	ALUE_0001723701	I
Aqu1.216869	Amphimedon queenslandica	Aqu1.216869	I
Bm3663	Brugia malayi	Bm3663	N
BTMF_0001641801	Brugia timori	BTMF_0001641801	N
BXY_1123500	Bursaphelenchus xylophilus	BXY_1123500	N
CBG02541	Caenorhabditis briggsae	CBG02541	I
CBN00477	Caenorhabditis brenneri	CBN00477	I
CBN16859	Caenorhabditis brenneri	CBN16859	I
CJA07640	Caenorhabditis japonica	CJA07640	I
CPIJ013489	Culex quinquefasciatus	CPIJ013489	I
CpipJ_CPIJ013489	Culex pipiens	CpipJ_CPIJ013489	I
CRE26587	Caenorhabditis remanei	CRE26587	N
EEL_0001066501	Elaeophora elaphi	EEL_0001066501	N
ENSAMXG00000013086	Astyanax mexicanus	ENSAMXG00000013086	I
ENSAPLG00000016417	Anas platyrhynchos	ENSAPLG00000016417	N
tead1a	Danio rerio	ENSDARG00000028159	I
tead1b	Gasterosteus aculeatus	ENSGACG00000015715	I
ENSGMOG00000002217	Gadus morhua	ENSGMOG00000002217	N
ENSLACG00000013349	Latimeria chalumnae	ENSLACG00000013349	I
ENSLOCG00000016688	Lepisosteus oculatus	ENSLOCG00000016688	I
Tead2	Mus musculus	ENSMUSG00000030796	D
TEAD2	Pteropus vampyrus	ENSPVAG00000010945	I
Tead2	Rattus norvegicus	ENSRNOG00000020695	I
TEAD1	Taeniopygia guttata	ENSTGUG00000015995	N
EVEC_0001129301	Enterobius vermicularis	EVEC_0001129301	N
sd	Drosophila melanogaster	FBgn0003345	D
GA21152	Drosophila pseudoobscura	FBgn0081140	I
GF20188	Drosophila ananassae	FBgn0097195	I
GG17919	Drosophila erecta	FBgn0110139	I
GH12522	Drosophila grimshawi	FBgn0120001	I
GI14876	Drosophila mojavensis	FBgn0137627	I
GL22923	Drosophila persimilis	FBgn0160513	I
GM22588	Drosophila sechellia	FBgn0177458	I
GJ19539	Drosophila virilis	FBgn0206682	I
GE17227	Drosophila yakuba	FBgn0234705	I
Gfo_R013616	Geospiza fortis	Gfo_R013616	N
GPLIN_000239200	Globodera pallida	GPLIN_000239200	N
HHAL001589-PA	Halyomorpha halys	HHAL001589-PA	I
ISCW001055	Ixodes scapularis	ISCW001055	N
L798_06691	Zootermopsis nevadensis	L798_06691	N
L889_g27469	Steinernema feltiae	L889_g27469	N
L892_g28430	Steinernema scapterisci	L892_g28430	N
L893_g28603	Steinernema glaseri	L893_g28603	N
L898_g3313	Steinernema monticolum	L898_g3313	N
LOAG_16930	Loa loa	LOAG_16930	N
maker-nMf.1.1.scaf11367-augustus-gene-0.3	Meloidogyne floridensis	maker-nMf.1.1.scaf11367-augustus-gene-0.3	N
MhA1_Contig1858.frz3.gene4	Meloidogyne hapla	MhA1_Contig1858.frz3.gene4	N
Minc08587	Meloidogyne incognita	Minc08587	N
nAv.1.0.1.g09844	Acanthocheilonema viteae	nAv.1.0.1.g09844	N
nDi.2.2.2.g03143	Dirofilaria immitis	nDi.2.2.2.g03143	N
nLs.2.1.2.g09869	Litomosoides sigmodontis	nLs.2.1.2.g09869	N
nOo.2.0.1.g04457	Onchocerca ochengi	nOo.2.0.1.g04457	N
Ocbimv22038896m.g	Octopus bimaculoides	Ocbimv22038896m.g	N
OFLC_0000413701	Onchocerca flexuosa	OFLC_0000413701	I
PHUM251000	Pediculus humanus	PHUM251000	N
PTRK_0001645900	Parastrongyloides trichosuri	PTRK_0001645900	N
RSKR_0000765700	Rhabditophanes kr3021	RSKR_0000765700	N
Sakowv30030097m.g	Saccoglossus kowalevskii	Sakowv30030097m.g	N
SPAL_0001147900	Strongyloides papillosus	SPAL_0001147900	N
SPAL_0001402900	Strongyloides papillosus	SPAL_0001402900	N
SSTP_0001098000	Strongyloides stercoralis	SSTP_0001098000	N
SVE_1986900	Strongyloides venezuelensis	SVE_1986900	N
TCLT_0000878101	Thelazia callipaeda	TCLT_0000878101	N
TMUE_s0021001300	Trichuris muris	TMUE_s0021001300	N
egl-44	Caenorhabditis elegans	WBGene00001208	I
WBGene00247728	Onchocerca volvulus	WBGene00247728	N
WUBG_04000	Wuchereria bancrofti	WUBG_04000	N
tead1	Xenopus tropicalis	XB-GENE-5909149	I
tead4	Xenopus tropicalis	XB-GENE-956369	I
XP_002943057	Xenopus tropicalis	XP_002943057	I

Rfx3 (Dipodomys ordii) RFX

TF Information

Directly determined binding motifs

Motifs from related TFs

DNA Binding Domains

Links

693 Related TFs

Rfx3 **(Dipodomys ordii)
RFX**