CIS-BP Database: Catalog of Inferred Sequence Binding Preferences
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otx1a
(
Danio rerio
)
Homeodomain
TF Information
Pfam ID
Interpro ID
Gene ID
CIS-BP ID
Sequence source
Animal TF db
PF00046 (Homeobox)
IPR001356
ENSDARG00000030703
T208578_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 brain development and retinal pigment epithelium development. Predicted to be active in nucleus. Is expressed in several structures, including anterior neural keel; axis; brain; immature eye; and neural plate. Orthologous to human OTX1 (orthodenticle homeobox 1). [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
Otx1
M00396_2.00
Mus musculus
NTAAKCYN
NRGMTTAN
PBM
Berger et al.(2008)
Otx1_2325
0.867
0.947
Otx2
M00418_2.00
Mus musculus
NTAAKMBN
NVKMTTAN
PBM
Berger et al.(2008)
Otx2_3441
0.867
0.947
OTX1
M03116_2.00
Homo sapiens
NNTAAKCGGATTANN
NNTAATCCGMTTANN
SELEX
Jolma et al.(2013)
OTX1_1
0.867
0.947
OTX1
M03117_2.00
Homo sapiens
NTAATCSB
VSGATTAN
SELEX
Jolma et al.(2013)
OTX1_2
0.867
0.947
OTX2
M03197_2.00
Homo sapiens
NHTAAKCGGATTANN
NNTAATCCGMTTADN
SELEX
Jolma et al.(2013)
OTX2_1
0.867
0.947
OTX2
M03198_2.00
Homo sapiens
HTAATCCB
VGGATTAD
SELEX
Jolma et al.(2013)
OTX2_2
0.867
0.947
Otx1
M03249_2.00
Mus musculus
NNTAAKCGGATTANN
NNTAATCCGMTTANN
SELEX
Jolma et al.(2013)
Otx1_1
0.867
0.947
Otx1
M03250_2.00
Mus musculus
NTAATCCN
NGGATTAN
SELEX
Jolma et al.(2013)
Otx1_2
0.867
0.947
OTX1
M05022_2.00
Homo sapiens
NTAATCCN
NGGATTAN
SELEX
Yin et al.(2017)
OTX1_eDBD_HT-SELEX
0.867
0.947
OTX1
M05024_2.00
Homo sapiens
NTAATCCNNN
NNNGGATTAN
SELEX
Yin et al.(2017)
OTX1_FL_HT-SELEX
0.867
0.947
OTX2
M05251_2.00
Homo sapiens
NTAATCCN
NGGATTAN
SELEX
Yin et al.(2017)
OTX2_FL_HT-SELEX
0.867
0.947
OTX2
M09153_2.00
Homo sapiens
BYTAATCCYYN
NRRGGATTARV
Misc
Kulakovskiy et al.(2013)
OTX2_HUMAN.H11MO.0.A
0.867
0.947
Otx2
M09183_2.00
Mus musculus
HTAATCCYNYNN
NNRNRGGATTAD
Misc
Kulakovskiy et al.(2013)
OTX2_MOUSE.H11MO.0.A
0.867
0.947
Otx2
M09569_2.00
Mus musculus
NHTAATCCHB
VDGGATTADN
Misc
Heinz et al.(2010)
EpiLC-Otx2_GSE56098
0.867
0.947
OTX1
M10673_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$OTX1_Q5
0.867
0.947
OTX2
M10727_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$OTX2_Q3_01
0.867
0.947
OTX2
M10728_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$OTX2_Q3
0.867
0.947
OTX1
M05023_2.00
Homo sapiens
NTAATCCN
NGGATTAN
SELEX
Yin et al.(2017)
OTX1_eDBD_Methyl-HT-SELEX
0.867
0.947
OTX1
M05025_2.00
Homo sapiens
HTAATCCNHN
NDNGGATTAD
SELEX
Yin et al.(2017)
OTX1_FL_Methyl-HT-SELEX
0.867
0.947
OTX2
M05252_2.00
Homo sapiens
NTAATCCN
NGGATTAN
SELEX
Yin et al.(2017)
OTX2_FL_Methyl-HT-SELEX
0.867
0.947
oc
M03808_2.00
Drosophila melanogaster
HTAATCCB
VGGATTAD
SELEX
Nitta et al.(2015)
oc_1
0.866
0.930
oc
M06502_2.00
Drosophila melanogaster
TAATCC
GGATTA
B1H
Mathelier et al.(2014)
MA0234.1
0.866
0.930
oc
M06282_2.00
Drosophila melanogaster
WTAATCC
GGATTAW
B1H
Zhu et al.(2011)
Oc_Cell_FBgn0004102
0.866
0.930
oc
M06283_2.00
Drosophila melanogaster
NTAATCCB
VGGATTAN
B1H
Zhu et al.(2011)
Oc_SOLEXA_FBgn0004102
0.866
0.930
oc
M09681_2.00
Drosophila melanogaster
HTAATCCN
NGGATTAD
Misc
Kulakovskiy et al.(2009)
oc
0.866
0.930
CRX
M00275_2.00
Homo sapiens
NMTAATCCSN
NSGGATTAKN
PBM
Barrera et al.(2016)
CRX_V66I
0.860
0.877
CRX
M00274_2.00
Homo sapiens
NMTAATCCSN
NSGGATTAKN
PBM
Barrera et al.(2016)
CRX_REF
0.851
0.860
Crx
M00489_2.00
Mus musculus
NWAAKMBN
NVKMTTWN
PBM
Berger et al.(2008)
Crx_3485
0.851
0.860
CRX
M04949_2.00
Homo sapiens
NTAATCCN
NGGATTAN
SELEX
Yin et al.(2017)
CRX_FL_HT-SELEX
0.851
0.860
Crx
M08139_2.00
Mus musculus
YTAATCCYCYY
RRGRGGATTAR
ChIP-seq
Mathelier et al.(2014)
MA0467.1
0.851
0.860
CRX
M09132_2.00
Homo sapiens
BYTAATCCBHYYN
NRRDVGGATTARV
Misc
Kulakovskiy et al.(2013)
CRX_HUMAN.H11MO.0.B
0.851
0.860
Crx
M09208_2.00
Mus musculus
BYTAATCCBHYYN
NRRDVGGATTARV
Misc
Kulakovskiy et al.(2013)
CRX_MOUSE.H11MO.0.A
0.851
0.860
Crx
M09577_2.00
Mus musculus
NYTAATCC
GGATTARN
Misc
Heinz et al.(2010)
Retina-Crx_GSE20012
0.851
0.860
CRX
M10647_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$CRX_Q4_01
0.851
0.860
CRX
M10648_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$CRX_Q4_02
0.851
0.860
CRX
M04950_2.00
Homo sapiens
HTAATCCN
NGGATTAD
SELEX
Yin et al.(2017)
CRX_FL_Methyl-HT-SELEX
0.851
0.860
CRX
M00273_2.00
Homo sapiens
NNYTAATCCVN
NBGGATTARNN
PBM
Barrera et al.(2016)
CRX_R90W
0.840
0.842
CRX
M00270_2.00
Homo sapiens
NWDAKNN
NNMTHWN
PBM
Barrera et al.(2016)
CRX_E80A
0.830
0.842
CRX
M00271_2.00
Homo sapiens
NHDAKNN
NNMTHDN
PBM
Barrera et al.(2016)
CRX_R41Q
0.818
0.842
CRX
M00272_2.00
Homo sapiens
NNHNATNN
NNATNDNN
PBM
Barrera et al.(2016)
CRX_R41W
0.818
0.842
ceh-37
M00674_2.00
Caenorhabditis elegans
HTAATCYN
NRGATTAD
PBM
Narasimhan et al.(2015)
pTH10716
0.794
0.684
Dmbx1
M00441_2.00
Mus musculus
NTAATCYNN
NNRGATTAN
PBM
Berger et al.(2008)
Dmbx1_2277
0.764
0.649
DMBX1
M03236_2.00
Homo sapiens
NHTAATCCBN
NVGGATTADN
SELEX
Jolma et al.(2013)
DMBX1_1
0.764
0.649
DMBX1
M05383_2.00
Homo sapiens
NTAATCSN
NSGATTAN
SELEX
Yin et al.(2017)
DMBX1_eDBD_HT-SELEX
0.764
0.649
DMBX1
M05384_2.00
Homo sapiens
HTAATCCN
NGGATTAD
SELEX
Yin et al.(2017)
DMBX1_eDBD_Methyl-HT-SELEX
0.764
0.649
ceh-53
M00679_2.00
Caenorhabditis elegans
HTAATCYN
NRGATTAD
PBM
Narasimhan et al.(2015)
pTH10699
0.760
0.526
ceh-36
M00673_2.00
Caenorhabditis elegans
NWAATCYN
NRGATTWN
PBM
Narasimhan et al.(2015)
pTH10730
0.759
0.649
HBX4_ECHGR
M02195_2.00
Echinococcus granulosus
NHTAATCYNN
NNRGATTADN
PBM
Weirauch et al.(2014)
pTH6301
0.750
0.561
NEMVEDRAFT_v1g113057
M02144_2.00
Nematostella vectensis
NYTAATCCBN
NVGGATTARN
PBM
Weirauch et al.(2014)
pTH6135
0.750
0.561
Gsc
M02120_2.00
Drosophila melanogaster
NTAATCYN
NRGATTAN
PBM
Weirauch et al.(2014)
pTH5511
0.741
0.614
Gsc
M03817_2.00
Drosophila melanogaster
TAATCCB
VGGATTA
SELEX
Nitta et al.(2015)
Gsc_1
0.741
0.614
Gsc
M03818_2.00
Drosophila melanogaster
TAATCGGATTA
TAATCCGATTA
SELEX
Nitta et al.(2015)
Gsc_2
0.741
0.614
Gsc
M03819_2.00
Drosophila melanogaster
TAATCYNHTAATCBN
NVGATTADNRGATTA
SELEX
Nitta et al.(2015)
Gsc_3
0.741
0.614
Gsc
M03820_2.00
Drosophila melanogaster
TAATCGGATTA
TAATCCGATTA
SELEX
Nitta et al.(2015)
Gsc_4
0.741
0.614
Gsc
M03821_2.00
Drosophila melanogaster
TAATCYNWTWATCYB
VRGATWAWNRGATTA
SELEX
Nitta et al.(2015)
Gsc_5
0.741
0.614
Gsc
M05873_2.00
Drosophila melanogaster
TAATCSNHTWA
TWADNSGATTA
SMiLE-seq
Isakova et al.(2017)
Gsc
0.741
0.614
Gsc
M06509_2.00
Drosophila melanogaster
TAATCY
RGATTA
B1H
Mathelier et al.(2014)
MA0190.1
0.741
0.614
Gsc
M06297_2.00
Drosophila melanogaster
VNTAATCY
RGATTANB
B1H
Zhu et al.(2011)
Gsc_Cell_FBgn0010323
0.741
0.614
Gsc
M06298_2.00
Drosophila melanogaster
NTAATCY
RGATTAN
B1H
Zhu et al.(2011)
Gsc_SOLEXA_FBgn0010323
0.741
0.614
Gsc
M00411_2.00
Mus musculus
NNTAATYBN
NVRATTANN
PBM
Berger et al.(2008)
Gsc_2327
0.736
0.579
GSC
M03146_2.00
Homo sapiens
NHTAATCCNH
DNGGATTADN
SELEX
Jolma et al.(2013)
GSC_1
0.736
0.579
GSC
M05134_2.00
Homo sapiens
NTAATCCB
VGGATTAN
SELEX
Yin et al.(2017)
GSC_eDBD_HT-SELEX
0.736
0.579
GSC
M05136_2.00
Homo sapiens
HTAATCCN
NGGATTAD
SELEX
Yin et al.(2017)
GSC_FL_HT-SELEX
0.736
0.579
GSC
M05135_2.00
Homo sapiens
HTAATCCB
VGGATTAD
SELEX
Yin et al.(2017)
GSC_eDBD_Methyl-HT-SELEX
0.736
0.579
GSC
M05137_2.00
Homo sapiens
HTAATCCN
NGGATTAD
SELEX
Yin et al.(2017)
GSC_FL_Methyl-HT-SELEX
0.736
0.579
CBG01820
M01241_2.00
Caenorhabditis briggsae
NTAATCCN
NGGATTAN
PBM
Lambert et al.(2019)
pTH11454
0.736
0.614
Pitx1
M00415_2.00
Mus musculus
NTAATCYNN
NNRGATTAN
PBM
Berger et al.(2008)
Pitx1_2312
0.731
0.614
PITX1
M03082_2.00
Homo sapiens
NHTAATCCN
NGGATTADN
SELEX
Jolma et al.(2013)
PITX1_1
0.731
0.614
PITX1
M03083_2.00
Homo sapiens
NHTAATCCN
NGGATTADN
SELEX
Jolma et al.(2013)
PITX1_2
0.731
0.614
PITX1
M03084_2.00
Homo sapiens
HTAATCCN
NGGATTAD
SELEX
Jolma et al.(2013)
PITX1_3
0.731
0.614
PITX1
M04928_2.00
Homo sapiens
NTAATCCN
NGGATTAN
SELEX
Yin et al.(2017)
PITX1_eDBD_HT-SELEX
0.731
0.614
PITX1
M04930_2.00
Homo sapiens
NTAATCCN
NGGATTAN
SELEX
Yin et al.(2017)
PITX1_FL_HT-SELEX
0.731
0.614
Pitx1
M09182_2.00
Mus musculus
NYWAAKCCYH
DRGGMTTWRN
Misc
Kulakovskiy et al.(2013)
PITX1_MOUSE.H11MO.0.C
0.731
0.614
PITX1
M10640_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$PITX1_Q4
0.731
0.614
PITX1
M10641_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$PITX1_Q6
0.731
0.614
PITX1
M04929_2.00
Homo sapiens
NTAAKCCN
NGGMTTAN
SELEX
Yin et al.(2017)
PITX1_eDBD_Methyl-HT-SELEX
0.731
0.614
PITX1
M04931_2.00
Homo sapiens
HTAATCCN
NGGATTAD
SELEX
Yin et al.(2017)
PITX1_FL_Methyl-HT-SELEX
0.731
0.614
PITX2
M00313_2.00
Homo sapiens
NWAAKHYN
NRDMTTWN
PBM
Barrera et al.(2016)
PITX2_REF
0.731
0.596
Pitx3
M00428_2.00
Mus musculus
NTAAKCYN
NRGMTTAN
PBM
Berger et al.(2008)
Pitx3_3497
0.731
0.596
Pitx2
M00440_2.00
Mus musculus
NTAATCCN
NGGATTAN
PBM
Berger et al.(2008)
Pitx2_2274
0.731
0.596
Ptx1
M02123_2.00
Drosophila melanogaster
NTAATCYNN
NNRGATTAN
PBM
Weirauch et al.(2014)
pTH5644
0.731
0.596
Ptx1
M00562_2.00
Drosophila melanogaster
NYTAATCCBN
NVGGATTARN
PBM
Busser et al.(2012a)
Ptx1
0.731
0.596
PITX3
M03111_2.00
Homo sapiens
NHTAATCCN
NGGATTADN
SELEX
Jolma et al.(2013)
PITX3_1
0.731
0.596
Ptx1
M03842_2.00
Drosophila melanogaster
NTAATCCN
NGGATTAN
SELEX
Nitta et al.(2015)
Ptx1_1
0.731
0.596
Ptx1
M03843_2.00
Drosophila melanogaster
NTAATCCN
NGGATTAN
SELEX
Nitta et al.(2015)
Ptx1_2
0.731
0.596
Ptx1
M03844_2.00
Drosophila melanogaster
NCGHTAATCCN
NGGATTADCGN
SELEX
Nitta et al.(2015)
Ptx1_3
0.731
0.596
PITX2
M05229_2.00
Homo sapiens
NTAAKCCN
NGGMTTAN
SELEX
Yin et al.(2017)
PITX2_eDBD_HT-SELEX
0.731
0.596
PITX2
M05231_2.00
Homo sapiens
NTAATCCN
NGGATTAN
SELEX
Yin et al.(2017)
PITX2_FL_HT-SELEX
0.731
0.596
PITX3
M04997_2.00
Homo sapiens
NTAATCCN
NGGATTAN
SELEX
Yin et al.(2017)
PITX3_eDBD_HT-SELEX
0.731
0.596
Ptx1
M06521_2.00
Drosophila melanogaster
YTAATCC
GGATTAR
B1H
Mathelier et al.(2014)
MA0201.1
0.731
0.596
Ptx1
M06319_2.00
Drosophila melanogaster
YTAATCC
GGATTAR
B1H
Zhu et al.(2011)
Ptx1_Cell_FBgn0020912
0.731
0.596
Ptx1
M06320_2.00
Drosophila melanogaster
NYTAATCC
GGATTARN
B1H
Zhu et al.(2011)
Ptx1_SOLEXA_FBgn0020912
0.731
0.596
PITX2
M10720_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$PITX2_Q2
0.731
0.596
PITX2
M10721_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$PITX2_Q4
0.731
0.596
PITX2
M10722_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$PITX2_Q6
0.731
0.596
PITX3
M10660_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$PITX3_Q2
0.731
0.596
PITX3
M10661_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$PITX3_Q3_01
0.731
0.596
PITX3
M10662_2.00
Homo sapiens
Transfac license required
Transfac license required
Transfac
Matys et al.(2006)
V$PITX3_Q3
0.731
0.596
PITX2
M00312_2.00
Homo sapiens
NNNTATWAATTNN
NNAATTWATANNN
PBM
Barrera et al.(2016)
PITX2_R130W
0.731
0.596
PITX2
M00314_2.00
Homo sapiens
NTAATMYN
NRKATTAN
PBM
Barrera et al.(2016)
PITX2_T114P
0.731
0.596
PITX2
M05230_2.00
Homo sapiens
HTAATCCN
NGGATTAD
SELEX
Yin et al.(2017)
PITX2_eDBD_Methyl-HT-SELEX
0.731
0.596
PITX2
M05232_2.00
Homo sapiens
YTAATCCY
RGGATTAR
SELEX
Yin et al.(2017)
PITX2_FL_Methyl-HT-SELEX
0.731
0.596
PITX3
M04998_2.00
Homo sapiens
NTAATCCN
NGGATTAN
SELEX
Yin et al.(2017)
PITX3_eDBD_Methyl-HT-SELEX
0.731
0.596
PITX2
M00310_2.00
Homo sapiens
HTAATCYN
NRGATTAD
PBM
Barrera et al.(2016)
PITX2_L100Q
0.731
0.579
GSC2
M03080_2.00
Homo sapiens
NHTAATCCBH
DVGGATTADN
SELEX
Jolma et al.(2013)
GSC2_1
0.731
0.561
GSC2
M04920_2.00
Homo sapiens
NTAATNNN
NNNATTAN
SELEX
Yin et al.(2017)
GSC2_eDBD_HT-SELEX
0.731
0.561
GSC2
M04921_2.00
Homo sapiens
NTAATCYN
NRGATTAN
SELEX
Yin et al.(2017)
GSC2_eDBD_Methyl-HT-SELEX
0.731
0.561
PITX2
M00311_2.00
Homo sapiens
TTAATCCY
RGGATTAA
PBM
Barrera et al.(2016)
PITX2_R108H
0.726
0.579
gsc
M09584_2.00
Xenopus tropicalis
NTAATCYN
NRGATTAN
Misc
Heinz et al.(2010)
FrogEmbryos-GSC_DRA000576
0.724
0.561
DPRX
M03237_2.00
Homo sapiens
NHTAATCYNN
NNRGATTADN
SELEX
Jolma et al.(2013)
DPRX_1
0.685
0.439
DPRX
M03238_2.00
Homo sapiens
NRGMTAATCYN
NRGATTAKCYN
SELEX
Jolma et al.(2013)
DPRX_2
0.685
0.439
DPRX
M05388_2.00
Homo sapiens
VGMTAATCYN
NRGATTAKCB
SELEX
Yin et al.(2017)
DPRX_eDBD_HT-SELEX
0.685
0.439
DPRX
M05389_2.00
Homo sapiens
AGATMATCYN
NRGATKATCT
SELEX
Yin et al.(2017)
DPRX_eDBD_Methyl-HT-SELEX
0.685
0.439
dve
M02122_2.00
Drosophila melanogaster
NTAATCCV
BGGATTAN
PBM
Weirauch et al.(2014)
pTH6218
0.632
0.368
AGAP006642
M02035_2.00
Anopheles gambiae
NHTAATCY
RGATTADN
PBM
Weirauch et al.(2014)
pTH6201
0.631
0.351
Obox6
M00490_2.00
Mus musculus
NTAATCYNN
NNRGATTAN
PBM
Berger et al.(2008)
Obox6_3440
0.616
0.351
For this family, TFs with SR scores >
0.599
will likely have a similar motif
DNA Binding Domains
Protein ID
Domain
From
To
Sequence
ENSDARP00000013327
Homeodomain
39
95
RRERTTFTRTQLDILESLFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQ
Links
Other
Homeodomain
family TFs
Other
Danio rerio
TFs
1141 Related TFs
Name
Species
Gene ID
Motif Evidence
SR
Score
Action
Invalid Input OrderBy