CIS-BP Database: Catalog of Inferred Sequence Binding Preferences
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rfx4
(
Danio rerio
)
RFX
TF Information
Pfam ID
Interpro ID
Gene ID
CIS-BP ID
Sequence source
Animal TF db
PF02257 (RFX_DNA_binding)
IPR003150
ENSDARG00000026395
T318191_2.00
Ensembl (2018-Dec-8)
Link out
NCBI Gene Info:
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within ventral midline development. Predicted to be located in nucleus. Is expressed in central nervous system and neural rod. Orthologous to human RFX4 (regulatory factor X4). [provided by Alliance of Genome Resources, Apr 2022]
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
RFX4
M02448_2.00
Cavia porcellus
GTHDYYNNGN
NCNNRRHDAC
PBM
Weirauch et al.(2014)
pTH9249
0.781
0.975
Rfx4
M00186_2.00
Mus musculus
GTHDYYNNSN
NSNNRRHDAC
PBM
Badis et al.(2009)
Rfx4_3761
0.781
0.975
RFX4
M03456_2.00
Homo sapiens
NGTWRYCATRGHWACN
NGTWDCYATGRYWACN
SELEX
Jolma et al.(2013)
RFX4_1
0.781
0.975
RFX4
M03457_2.00
Homo sapiens
NGTTGCYRRGCAACS
SGTTGCYYRGCAACN
SELEX
Jolma et al.(2013)
RFX4_2
0.781
0.975
RFX4
M05721_2.00
Homo sapiens
BGTWRYCATGRYWACV
BGTWRYCATGRYWACV
SELEX
Yin et al.(2017)
RFX4_eDBD_HT-SELEX
0.781
0.975
RFX4
M05722_2.00
Homo sapiens
BGTWRYCATGRYWACV
BGTWRYCATGRYWACV
SELEX
Yin et al.(2017)
RFX4_eDBD_Methyl-HT-SELEX
0.781
0.975
Rfx6
M09365_2.00
Mus musculus
BDGTWKCYNDG
CHNRGMAACHV
Misc
Kulakovskiy et al.(2013)
RFX6_MOUSE.H11MO.0.C
0.717
0.696
Rfx3
M00188_2.00
Mus musculus
SNTRRHDACN
NGTHDYYANS
PBM
Badis et al.(2009)
Rfx3_3961
0.714
0.684
Rfx3
M03463_2.00
Mus musculus
SGTTRCCATGGYAACS
SGTTRCCATGGYAACS
SELEX
Jolma et al.(2013)
Rfx3_1
0.714
0.684
Rfx3
M09368_2.00
Mus musculus
BBGTTGCCATGGNRAC
GTYNCCATGGCAACVV
Misc
Kulakovskiy et al.(2013)
RFX3_MOUSE.H11MO.0.C
0.714
0.684
RFX2
M02449_2.00
Homo sapiens
BGTHRYYADG
CHTRRYDACV
PBM
Weirauch et al.(2014)
pTH9194
0.713
0.671
RFX2
M02450_2.00
Ornithorhynchus anatinus
NGTHRYYANV
BNTRRYDACN
PBM
Weirauch et al.(2014)
pTH9269
0.713
0.671
RFX1
M02447_2.00
Anolis carolinensis
GTHRCYANGN
NCNTRGYDAC
PBM
Weirauch et al.(2014)
pTH9223
0.712
0.646
RFX1
M02451_2.00
Tetraodon nigroviridis
GTHDYYANGN
NCNTRRHDAC
PBM
Weirauch et al.(2014)
pTH9385
0.712
0.646
RFX1
M05723_2.00
Homo sapiens
BGTTRYCATGRYAACV
BGTTRYCATGRYAACV
SELEX
Yin et al.(2017)
RFX1_eDBD_HT-SELEX
0.712
0.646
Rfx1
M08162_2.00
Mus musculus
GTTGCYADGGNRAC
GTYNCCHTRGCAAC
ChIP-seq
Mathelier et al.(2014)
MA0509.1
0.712
0.646
RFX1
M09363_2.00
Homo sapiens
BBBSSNGTTGCCADGGNRMCVV
BBGKYNCCHTGGCAACNSSVVV
Misc
Kulakovskiy et al.(2013)
RFX1_HUMAN.H11MO.0.B
0.712
0.646
Rfx1
M09367_2.00
Mus musculus
BBBSSNGTTGCCADGGNRMCVV
BBGKYNCCHTGGCAACNSSVVV
Misc
Kulakovskiy et al.(2013)
RFX1_MOUSE.H11MO.0.A
0.712
0.646
RFX1
M11245_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$EFC_Q6
0.712
0.646
RFX1
M11246_2.00
Homo sapiens
HNGTTRCYWVGYDMYNN
NNRKHRCBWRGYAACND
Transfac
Matys et al.(2006)
V$RFX1_01
0.712
0.646
RFX1
M11247_2.00
Homo sapiens
HNGTTRCYWBVGYDMYNN
NNRKHRCBVWRGYAACND
Transfac
Matys et al.(2006)
V$RFX1_02
0.712
0.646
RFX1
M11248_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$RFX1_Q6
0.712
0.646
RFX1
M05724_2.00
Homo sapiens
BGTWRYCATGRYWACV
BGTWRYCATGRYWACV
SELEX
Yin et al.(2017)
RFX1_eDBD_Methyl-HT-SELEX
0.712
0.646
XP_002157607.1
M02456_2.00
Hydra magnipapillata
GTHDYYDNVN
NBNHRRHDAC
PBM
Weirauch et al.(2014)
pTH9199
0.711
0.646
G4VLF2_SCHMA
M02452_2.00
Schistosoma mansoni
GTTGCTAD
HTAGCAAC
PBM
Weirauch et al.(2014)
pTH8587
0.709
0.620
GB41876
M02453_2.00
Apis mellifera
GTHDCYANVN
NBNTRGHDAC
PBM
Weirauch et al.(2014)
pTH9226
0.709
0.646
Sjc_0102030
M02455_2.00
Schistosoma japonicum
GTTRCYANG
CNTRGYAAC
PBM
Weirauch et al.(2014)
pTH9285
0.708
0.608
Rfx
M03959_2.00
Drosophila melanogaster
NGTHRCYATRGYDACN
NGTHRCYATRGYDACN
SELEX
Nitta et al.(2015)
Rfx_1
0.708
0.608
Rfx
M03960_2.00
Drosophila melanogaster
GTTGCTARGCAAC
GTTGCYTAGCAAC
SELEX
Nitta et al.(2015)
Rfx_2
0.708
0.608
Rfx
M03961_2.00
Drosophila melanogaster
BGTWRCCATGGYWACV
BGTWRCCATGGYWACV
SELEX
Nitta et al.(2015)
Rfx_3
0.708
0.608
Rfx
M03962_2.00
Drosophila melanogaster
GTTRCYAWTRGYAAC
GTTRCYAWTRGYAAC
SELEX
Nitta et al.(2015)
Rfx_4
0.708
0.608
Rfx
M03963_2.00
Drosophila melanogaster
GTTGCTARGCAAC
GTTGCYTAGCAAC
SELEX
Nitta et al.(2015)
Rfx_5
0.708
0.608
Rfx2
M03461_2.00
Mus musculus
BGTTRCCATGGYAACV
BGTTRCCATGGYAACV
SELEX
Jolma et al.(2013)
Rfx2_1
0.704
0.633
Rfx2
M03462_2.00
Mus musculus
SGTTGCTARGCAACV
BGTTGCYTAGCAACS
SELEX
Jolma et al.(2013)
Rfx2_2
0.704
0.633
Rfx2
M05888_2.00
Mus musculus
NGTTRCYATGGHDAY
RTHDCCATRGYAACN
SMiLE-seq
Isakova et al.(2017)
RFX2
0.704
0.633
Rfx2
M09366_2.00
Mus musculus
NBYBGTYNCCMTGGCAACNSSS
SSSNGTTGCCAKGGNRACVRVN
Misc
Kulakovskiy et al.(2013)
RFX2_MOUSE.H11MO.0.A
0.704
0.633
RFX3
M03452_2.00
Homo sapiens
NGTTRCCATGGHAACV
BGTTDCCATGGYAACN
SELEX
Jolma et al.(2013)
RFX3_1
0.704
0.646
RFX3
M03453_2.00
Homo sapiens
BGTTGCTARGCAACS
SGTTGCYTAGCAACV
SELEX
Jolma et al.(2013)
RFX3_2
0.704
0.646
RFX3
M02750_2.00
Homo sapiens
GTTRYYATGG
CCATRRYAAC
SELEX
Jolma et al.(2010)
RFX3_dimer
0.704
0.646
RFX3
M05715_2.00
Homo sapiens
NGTTRYYATRRYAACN
NGTTRYYATRRYAACN
SELEX
Yin et al.(2017)
RFX3_eDBD_HT-SELEX_1
0.704
0.646
RFX3
M05716_2.00
Homo sapiens
BGTTGCTARGCAACS
SGTTGCYTAGCAACV
SELEX
Yin et al.(2017)
RFX3_eDBD_HT-SELEX_2
0.704
0.646
RFX3
M09361_2.00
Homo sapiens
BGTTRCCATGGYRN
NYRCCATGGYAACV
Misc
Kulakovskiy et al.(2013)
RFX3_HUMAN.H11MO.0.B
0.704
0.646
RFX3
M09627_2.00
Homo sapiens
BNGTTGCCATGGCAAC
GTTGCCATGGCAACNV
Misc
Heinz et al.(2010)
K562-RFX3_SRA012198
0.704
0.646
RFX3
M05717_2.00
Homo sapiens
BGTTRYYATRRYAACV
BGTTRYYATRRYAACV
SELEX
Yin et al.(2017)
RFX3_eDBD_Methyl-HT-SELEX_1
0.704
0.646
RFX3
M05718_2.00
Homo sapiens
BGTTGCTARGCAACV
BGTTGCYTAGCAACV
SELEX
Yin et al.(2017)
RFX3_eDBD_Methyl-HT-SELEX_2
0.704
0.646
daf-19
M00709_2.00
Caenorhabditis elegans
SGTTRCTADG
CHTAGYAACS
PBM
Narasimhan et al.(2015)
pTH10021
0.704
0.608
RFX2
M03454_2.00
Homo sapiens
BGTTRCCATGGYAACV
BGTTRCCATGGYAACV
SELEX
Jolma et al.(2013)
RFX2_1
0.703
0.633
RFX2
M03455_2.00
Homo sapiens
SGTTGCTARGCAACS
SGTTGCYTAGCAACS
SELEX
Jolma et al.(2013)
RFX2_2
0.703
0.633
RFX2
M05719_2.00
Homo sapiens
NGTWDYYATRRHWACN
NGTWDYYATRRHWACN
SELEX
Yin et al.(2017)
RFX2_eDBD_HT-SELEX
0.703
0.633
RFX2
M09362_2.00
Homo sapiens
YNGTTGCCATGGVRACVV
BBGTYBCCATGGCAACNR
Misc
Kulakovskiy et al.(2013)
RFX2_HUMAN.H11MO.0.A
0.703
0.633
RFX2
M09628_2.00
Homo sapiens
BGTTKCCATGGMAAC
GTTKCCATGGMAACV
Misc
Heinz et al.(2010)
LoVo-RFX2_GSE49402
0.703
0.633
RFX2
M05720_2.00
Homo sapiens
BGTTRCCATGRYAACV
BGTTRYCATGGYAACV
SELEX
Yin et al.(2017)
RFX2_eDBD_Methyl-HT-SELEX
0.703
0.633
PHUM046580
M02454_2.00
Pediculus humanus
NGTHDCYANV
BNTRGHDACN
PBM
Weirauch et al.(2014)
pTH9278
0.699
0.646
RFX1
M00066_2.00
Saccharomyces cerevisiae
NSGTTGCYAN
NTRGCAACSN
PBM
Badis et al.(2008)
RFX1_4537
0.651
0.418
RFX1
M07494_2.00
Saccharomyces cerevisiae
BGTTRCYA
TRGYAACV
PBM, CSA and or DIP-chip
Mathelier et al.(2014)
MA0365.1
0.651
0.418
RFX1
M08600_2.00
Saccharomyces cerevisiae
CGTYRBYAYRGYWACM
KGTWRCYRTRVYRACG
Misc
DeBoer et al.(2011)
YLR176C_1478
0.651
0.418
RFX1
M08601_2.00
Saccharomyces cerevisiae
BGTTRCYA
TRGYAACV
Misc
DeBoer et al.(2011)
YLR176C_496
0.651
0.418
RFX1
M11251_2.00
Saccharomyces cerevisiae
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
F$RFX1_02
0.651
0.418
For this family, TFs with SR scores >
0.650
will likely have a similar motif
DNA Binding Domains
Protein ID
Domain
From
To
Sequence
ENSDARP00000032295
RFX
58
136
TPATLQWLEENYEIAEGVCIPRSALYMHYLDFCEKLDSQPVNAASFGKIIRQQFPQLTTRRLGTRGQSKYHYYGIAVKE
Links
Other
RFX
family TFs
Other
Danio rerio
TFs
618 Related TFs
Name
Species
Gene ID
Motif Evidence
SR
Score
Action
Invalid Input OrderBy