CIS-BP Database: Catalog of Inferred Sequence Binding Preferences
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PIF1
(
Arabidopsis thaliana
)
bHLH
TF Information
Pfam ID
Interpro ID
Gene ID
CIS-BP ID
Sequence source
Animal TF db
PF00010 (HLH)
IPR001092
AT2G20180
T030618_2.00
Ensembl (2018-Dec-8)
Link out
NCBI Gene Info:
Encodes a novel Myc-related bHLH transcription factor that has transcriptional activation activity in the dark. It is a key negative regulator of phytochrome-mediated seed germination and acts by inhibiting chlorophyll biosynthesis, light-mediated suppression of hypocotyl elongation and far-red light-mediated suppression of seed germination, and promoting negative gravitropism in hypocotyls. Light reduces this activity in a phy-dependent manner. The protein preferentially interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB), is physically associated with APRR1/TOC1 and is degraded in red (R) and far-red (FR) light through the ubiquitin (ub)-26S proteasome pathway to optimize photomorphogenic development in Arabidopsis. It also negatively regulates GA3 oxidase expression.
Directly determined binding motifs
Name/Motif ID
Species
Forward
Reverse
Type/Study/Study ID
SR
Score
DBD
Identity
PIF1
M01703_2.00
Arabidopsis thaliana
NNCACGTGNN
NNCACGTGNN
PBM
Weirauch et al.(2014)
pTH8733
(Direct)
(Direct)
PIF1
M08404_2.00
Arabidopsis thaliana
NCACGTGWSNYNHH
DDNRNSWCACGTGN
ChIP-chip
Mathelier et al.(2014)
MA0552.1
(Direct)
(Direct)
PIF1
M09783_2.00
Arabidopsis thaliana
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
P$PIF1_01
(Direct)
(Direct)
Motifs from related TFs
Name/Motif ID
Species
Forward
Reverse
Type/Study/Study ID
SR
Score
DBD
Identity
PIF4
M08046_2.00
Arabidopsis thaliana
CACGTGSV
BSCACGTG
ChIP-seq
Mathelier et al.(2014)
MA0561.1
0.871
0.860
PIF3
M00854_2.00
Arabidopsis thaliana
CACGTGSNN
NNSCACGTG
PBM
Franco-Zorrilla et al.(2014)
PIF3
0.868
0.860
PIF3
M00722_2.00
Arabidopsis thaliana
NCACRTN
NAYGTGN
PBM
Chang et al.(2013)
pTH8200
0.868
0.860
PK05451.1
M01120_2.00
Cannabis sativa
YCACGTGM
KCACGTGR
PBM
Lambert et al.(2019)
pTH10100
0.868
0.860
PIF3
M08045_2.00
Arabidopsis thaliana
HCACGTGGVH
DBCCACGTGD
ChIP-seq
Mathelier et al.(2014)
MA0560.1
0.868
0.860
PIF3
M09780_2.00
Arabidopsis thaliana
BDRRRVCACGTGRVSHCD
HGDSBYCACGTGBYYYHV
Transfac
Matys et al.(2006)
P$PIF3_01
0.868
0.860
PIF3
M09781_2.00
Arabidopsis thaliana
DDDVCCACGTGGVMVNB
VNBKBCCACGTGGBHHH
Transfac
Matys et al.(2006)
P$PIF3_02
0.868
0.860
PIF5
M08047_2.00
Arabidopsis thaliana
YCACRTGS
SCAYGTGR
ChIP-seq
Mathelier et al.(2014)
MA0562.1
0.859
0.840
PIF5
M09452_2.00
Arabidopsis thaliana
NNBCAYGTGV
BCACRTGVNN
Misc
Heinz et al.(2010)
Arabidopsis-PIF5ox_GSE35062
0.859
0.840
e_gw1.209.40.1
M01756_2.00
Physcomitrella patens
NNCACGTGNN
NNCACGTGNN
PBM
Weirauch et al.(2014)
pTH8070
0.845
0.640
LRL2
M06738_2.00
Arabidopsis thaliana
CACGTGSVDMNCACG
CGTGNKHBSCACGTG
Dap-seq
OMalley et al.(2016)
bHLH69_col_a
0.845
0.600
SPT
M01709_2.00
Arabidopsis thaliana
NCACGTGSN
NSCACGTGN
PBM
Weirauch et al.(2014)
pTH8111
0.844
0.800
For this family, TFs with SR scores >
0.838
will likely have a similar motif
Experimental Constructs
Motif ID
Domain
From
To
Sequence
M01703_2.00
bHLH
51
100
AAEVHNLSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQ
DNA Binding Domains
Protein ID
Domain
From
To
Sequence
AT2G20180.1
bHLH
214
263
AAEVHNLSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQ
AT2G20180.2
bHLH
285
334
AAEVHNLSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQ
AT2G20180.3
bHLH
285
334
AAEVHNLSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQ
AT2G20180.4
bHLH
285
334
AAEVHNLSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQ
AT2G20180.5
bHLH
214
263
AAEVHNLSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQ
AT2G20180.6
bHLH
285
334
AAEVHNLSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQ
AT2G20180.7
bHLH
214
263
AAEVHNLSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQ
AT2G20180.8
bHLH
285
334
AAEVHNLSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQ
Links
Other
bHLH
family TFs
Other
Arabidopsis thaliana
TFs
470 Related TFs
Name
Species
Gene ID
Motif Evidence
SR
Score
Action
Invalid Input OrderBy