Motif Tools
Motif family atlas

What binds this motif?

163 families, 4232 motifs, four databases. A family here is a set of motifs it is reasonable to treat as the same motif — usually one DNA-binding-domain family whose members cannot be told apart from sequence alone. Each page says what binds the site, what the sequence means structurally, and what a hit does and does not let you conclude.

The factor name attached to a motif is a claim, not a fact: ChIP-derived motifs can belong to a partner protein, some database entries are inherited from a non-human orthologue, and paralogues in one family are usually indistinguishable. Every page is explicit about which of these applies.

See where the data disagrees with the label →

C2H2 zinc finger

50 families · 1580 motifs
587
KRAB zinc-finger proteins (KZFPs)
GCTCCCTGC
KRAB zinc-finger proteins (KZFPs) are the largest family of DNA-binding proteins in the human genome: roughly 350 to 380 genes, most named only ZNF followed by a number.
256
Unnamed zinc-finger archetypes
CCtCaGCCTCC
Not a motif but a label gap.
168
Other C2H2 zinc fingers
ccCgGCCTCC
The remainder of the C2H2 zinc-finger class: factors that are neither KRAB zinc-finger proteins nor members of a family with its own entry.
100
KLF / SP (GC-box)
GGGGCGGGG
The SP and KLF proteins are about 26 human transcription factors that each use three C2H2 zinc fingers to read a nine- to ten-base GC-rich element.
60
Other BTB-ZF (ZBTB)
CTgGAAC
BTB-ZF proteins, also called POZ-ZF, pair an N-terminal BTB/POZ domain, a dimerization module, with a short C2H2 zinc-finger array.
48
SCAN-domain zinc fingers (ZSCAN/ZKSCAN)
GGAgGTGAG
The larger, thinner-documented half of the human SCAN-domain zinc fingers: 26 labels including ZSCAN1, 2, 5, 9, 12, 16, 23, 25, 26, 30 and 31, ZKSCAN2, 4, 5, 7 and 8, and the older names ZNF165, ZNF174, ZNF232, ZNF396, ZNF444 and ZNF449.
27
GLI
GACCACCCA
GLI factors are five-fingered C2H2 zinc-finger proteins that read the nine-base site GACCACCCA and form the transcriptional output of the Hedgehog pathway.
27
PRDM
ACTTTCaCT
PRDM proteins are zinc-finger transcription factors defined by an N-terminal PR domain, a variant of the SET methyltransferase fold, followed by a tandem array of C2H2 zinc fingers that does the DNA binding.
24
ZIC
GACCCCCCGCTGTG
ZIC1 to ZIC5 are five-fingered C2H2 zinc-finger proteins whose DNA-binding domains are the closest relatives of GLI outside the GLIS subfamily, and which read a GLI-like site.
24
ZNF24 / ZSCAN-type promoter ZFs
GTCTACACnG
A small group of SCAN-domain C2H2 zinc fingers with defined, experimentally supported binding sites at promoters and microsatellites: ZNF24 (also known as ZNF191 and ZSCAN3), ZSCAN4, ZSCAN21, ZSCAN22, ZSCAN29, ZKSCAN1 and ZKSCAN3.
18
SNAIL / SCRATCH
CAGGTG
The SNAIL/SCRATCH proteins - SNAI1 (Snail), SNAI2 (Slug), SNAI3 (Smuc), SCRT1 and SCRT2 - are C2H2 zinc-finger repressors that read the E-box CAGGTG, the same 6 bp core that basic helix-loop-helix activators use.
15
EGR
GCGTGGGCG
EGR1 to EGR4 are immediate-early transcription factors whose three C2H2 zinc fingers read a nine-base GC-rich site, GCGTGGGCG, also written GCGGGGGCG.
14
YY1 / YY2
CGCCATNTT
YY1 is a ubiquitously expressed zinc-finger protein that binds a short CCAT-centered site, usually written CGCCATNTT or, on the other strand, AANATGGCGGC.
12
ZBTB7A/B/C (LRF)
CGACCACC
ZBTB7A, ZBTB7B and ZBTB7C are BTB/POZ zinc-finger proteins that read short GC-rich sites through four C2H2 fingers and repress or reorganize promoters through the dimerizing BTB domain.
10
CTCF
CCASYAGRKGGCRSYR
CTCF is a single, near-ubiquitously expressed protein whose eleven C2H2 zinc fingers read an asymmetric, roughly 15-20 bp GC-rich sequence, often with a second recognition module a few bases upstream.
9
GFI1 / GFI1B
TAAATCACWGC
GFI1 and GFI1B are six-fingered C2H2 zinc-finger repressors of blood cell development that bind a well-defined AATC-core site, TAAATCAC(A/T)GC.
9
ZNF143 / THAP11 (SBS)
ACTACAATTCCC
The SPH element, also called the SBS, is a promoter element read by three proteins that are not close relatives.
9
OVOL (OVO-like)
CCGTTA
OVOL1 and OVOL2 are C2H2 zinc-finger repressors, the mammalian counterparts of Drosophila OVO/shavenbaby, that bind a short AT-flanked core, CCGTTA (equivalently TAACGG on the other strand).
8
MAZ / PATZ1
GGGAGGG
MAZ, the Myc-associated zinc finger protein, and PATZ1 are broadly expressed C2H2 zinc-finger proteins that bind short G-rich runs, written GGGAGGG or GGGGAGGGG and read as CCCTCCCC on the opposite strand.
8
HIC1 / HIC2
SNGSGGGCAMCC
HIC1 (hypermethylated in cancer 1) and HIC2 are BTB/POZ zinc-finger repressors with five Kruppel-like C2H2 fingers.
8
IKZF (Ikaros)
GGGAA
The Ikaros family (IKZF1 Ikaros, IKZF2 Helios, IKZF3 Aiolos, IKZF4 Eos, IKZF5 Pegasus) are lymphoid zinc-finger proteins with an N-terminal C2H2 array that binds DNA and a C-terminal pair of fingers that mediates homo- and heterodimerization.
8
BCL11A / BCL11B
TGACCA
BCL11A and BCL11B (originally CTIP1 and CTIP2) are paralogous C2H2 zinc-finger repressors with six fingers, of which a C-terminal cluster binds DNA while the N-terminal region recruits NuRD.
8
ZNF460 / ZNF317-like
AGTCtGCTGT
ZNF460 and ZNF317 are poorly characterized human C2H2 zinc-finger proteins grouped here because their database motifs cluster together, not because a published experiment showed they read the same sequence.
8
HINFP (MIZF)
CGGACGTT
HINFP, also called HiNF-P and originally cloned as MIZF, is a seven-finger C2H2 zinc-finger protein that reads a short CGGAC core, usually written CGGACGTT.
8
PLAG / PLAGL
GRGGCNNNNNNGGG
The PLAG proteins - PLAG1, PLAGL1 (also called ZAC1 or LOT1) and PLAGL2 - are C2H2 zinc-finger factors with seven fingers that read a bipartite G-rich site: a GRGGC core and a GGG cluster separated by roughly six to eight base pairs.
8
OSR1 / OSR2
GCTACTGT
OSR1 and OSR2 (odd-skipped related 1 and 2) are the two vertebrate members of the Odd family of C2H2 zinc-finger proteins, homologs of Drosophila odd-skipped.
7
BCL6 / BCL6B
TTCCTAGAA
BCL6 and its paralogue BCL6B (BAZF) are BTB/POZ zinc-finger repressors that bind a nine-base site, TTCCTAGAA, which is a TTCNNNGAA element of the same class that STAT dimers use.
6
ZNF263
GGAGGAGGAGGAGGA
ZNF263 is a nine-finger C2H2 zinc-finger protein that also carries a KRAB repression domain and a SCAN oligomerization domain.
6
ZNF281 / ZNF148 (ZBP-89)
GGGGGAGGGG
ZNF148 (better known as ZBP-89) and ZNF281 (ZBP-99) are broadly expressed four-fingered C2H2 proteins that bind GC- and GA-rich promoter elements, most often written GGGGGAGGGG or, on the opposite strand, CCCCTCCCCC; longer models add a CCCCACCCC module.
6
Transposase-derived / TE-binding zinc fingers
CwgacbgCCTGCC
A small entry for KRAB zinc fingers whose recognized sequence is itself a piece of a transposable element.
5
WT1
GCGTGGGAGT
WT1 is the Wilms tumor suppressor, a four-fingered C2H2 zinc-finger protein whose last three fingers are closely related to those of EGR1 and which binds essentially the same GC-rich site.
5
ZEB
CACCTG
ZEB1 and ZEB2 are large C2H2 zinc-finger repressors that bind the E-box-like sequence CACCTG, written CAGGTG when read on the other strand.
5
ZNF384 / ZNF362
AAAAAAAA
ZNF384 and its near-identical paralogue ZNF362 are C2H2 zinc-finger proteins that bind homopolymeric runs of A on one strand and T on the other.
5
ZNF768
CTtaaCCTCTCTGaG
ZNF768 is a C2H2 zinc-finger protein whose binding site sits in the core region of mammalian-wide interspersed repeats (MIRs), an old family of SINE retrotransposons.
5
MTF1
TGCRCNC
MTF1 (MTF-1) is a six-finger C2H2 zinc-finger protein that binds the metal response element, a short TGCRCNC core first defined as the 12-base-pair repeat that makes metallothionein promoters metal-inducible.
5
ZFP57 / imprinting
TGCCGC
ZFP57 is a KRAB zinc-finger protein that reads a six-base sequence, TGCCGC, but only when the CpG inside it is methylated.
4
REST (NRSF)
TTCAGCACCACGGACAGCGCC
REST, also called NRSF, is a single zinc-finger protein that recognizes RE1 (the neuron- restrictive silencer element), a 21-base-pair site that is one of the longest and most information- rich transcription-factor motifs in the human genome.
4
ZBTB33 (Kaiso)
TCCTGCNA
ZBTB33, better known as Kaiso, is a BTB/POZ zinc-finger repressor with only three C2H2 fingers and two distinct ways of reading DNA.
4
MECOM / EVI1
GAYAAGAYAAGATAA
MECOM, better known as EVI1, is a 145-kDa C2H2 zinc-finger protein with two separate finger clusters that bind two different sequences.
4
ZFX / ZFY
GCCBMGGCCT
ZFX and its Y-linked paralogue ZFY are thirteen-finger C2H2 zinc-finger activators that bind a short GC-rich site containing a GGCCT core.
4
ZNF410
CATCCCATAATA
ZNF410 is a five-finger C2H2 zinc-finger protein that recognizes a long, information-rich element, and it is the clearest known case of a mammalian transcription factor with essentially one target gene.
4
VEZF1
CCCCCCac
VEZF1, originally cloned twice as DB1 and as Vezf1, is a broadly expressed six-fingered C2H2 zinc-finger protein first defined on CT/GC-rich promoter elements and on the chicken beta-globin HS4 insulator, where its sites protect against DNA methylation.
3
CTCFL (BORIS)
CCASYAGRKGGCRSYR
CTCFL, usually called BORIS, is the single paralogue of CTCF.
3
INSM1 / INSM2
TGTCAGGGGGCG
INSM1 (originally IA-1, cloned from a human insulinoma) and its paralogue INSM2 are five-fingered C2H2 zinc-finger repressors of neuroendocrine and neuronal differentiation.
3
ZBTB18 (RP58)
MACATCTGKM
ZBTB18, first described as RP58, is a BTB/POZ zinc-finger repressor that binds an E-box-like site, (A/C)ACATCTG(G/T)(A/C), whose CATCTG core reads CAGATG on the opposite strand.
3
SALL
rGGGtGGGG
SALL1 to SALL4 are the human Spalt-like proteins: large C2H2 zinc-finger factors built from several clusters of paired fingers, with a short N-terminal motif that recruits the NuRD corepressor complex.
3
RREB1
CCCCAAACCACCCC
RREB1 is a large C2H2 zinc-finger protein, originally identified as the factor binding the RAS-responsive element of the human calcitonin promoter in medullary thyroid carcinoma cells.
2
ZBTB17 (MIZ1)
AATCGATT
ZBTB17, universally called MIZ1, is a BTB/POZ protein with an unusually long array of C2H2 zinc fingers that binds core-promoter regions around transcription start sites.
2
GTF3A (TFIIIA)
CTCCCATCC
GTF3A encodes TFIIIA, the transcription factor in which the C2H2 zinc finger was first recognized, and the protein that made the zinc finger a general concept.
1
CASZ1 (castor)
TTTTgGGgnaaAatnngnndtTT
CASZ1 is the single human orthologue of Drosophila castor, a large multi-zinc-finger transcription factor that in flies specifies a late temporal window of neuroblast identity.

Homeodomain

9 families · 552 motifs
275
Q50 homeodomain (DLX/MSX/LHX-type, TAATTA)
TAATTA
About half of the roughly 200 human homeodomain proteins carry glutamine at position 50 of the domain and read the palindromic hexamer TAATTA.
75
Anterior HOX (HOX1-8)
TAATTA
The 39 human HOX genes sit in four clusters and specify position along the head-to-tail axis.
63
Posterior HOX (HOX9-13, AbdB-like)
TTTTACGAC
HOX paralogue groups 9 to 13 - the Abdominal-B-like or posterior HOX proteins - read a different core from the rest of the homeodomain superfamily.
51
NKX
TAAGTG
NKX proteins are homeodomain transcription factors related to Drosophila tinman and vnd, and they are the main exception to the rule that homeodomains read a TAAT core.
34
K50 homeodomain (OTX/PITX/CRX-type, TAATCC)
TAATCC
A small group of homeodomains carries lysine instead of glutamine at position 50 of the domain, and that single substitution changes the two base pairs read 3' of the invariant TAAT core from TA to CC.
17
CDX / PDX / anterior gut HD
TTTATG
This family groups the caudal-related factors CDX1, CDX2 and CDX4 with PDX1, all encoded by ParaHox genes - an ancient cluster that is the evolutionary sister of the Hox cluster.
16
PRD-like / primate-specific (CRX-like)
TAATCC
PRD-like homeobox genes are a small set of rapidly evolving, single-homeodomain factors, ARGFX, DPRX, LEUTX, TPRX1 and RHOXF1/2 among them, that are expressed almost exclusively in the oocyte, the cleavage-stage embryo and the germ line.
13
Atypical / composite homeodomain
TAACTAG
This family collects homeodomains that do not behave like homeodomains.
8
DUX / DUXA
TAATCTAATCA
DUX4 and its relatives DUXA and DUXB carry two homeodomains in tandem within a single polypeptide, an architecture found only in placental mammals and derived from a retrotransposed copy of an ancestral homeobox gene.

Nuclear receptor

12 families · 239 motifs
106
RXR and its heterodimers
AGGTCA
This family covers retinoid X receptors (RXRA/B/G) and the receptors that heterodimerize with them: retinoic acid receptors (RARA/B/G), thyroid hormone receptors (THRA/THRB), the vitamin D receptor (VDR), the PPARs, the liver X receptors (NR1H2/NR1H3), FXR (NR1H4) and the xenobiotic sensors PXR and CAR (NR1I2/NR1I3).
21
Steroid receptors (GR/MR/PR/AR)
AGwACAtnaTGTtCc
The steroid receptors - glucocorticoid receptor (GR/NR3C1), mineralocorticoid receptor (MR/NR3C2), progesterone receptor (PGR) and androgen receptor (AR) - are hormone-activated transcription factors that bind DNA as homodimers on a 15 bp inverted repeat: two copies of the hexamer AGAACA facing each other across a 3 bp spacer, written AGAACAnnnTGTTCT.
21
COUP-TF (NR2F)
AaAGGTCA
COUP-TFI (NR2F1), COUP-TFII (NR2F2) and EAR2 (NR2F6) are orphan nuclear receptors that bind DNA as homodimers, most often on a DR1: two AGGTCA half-sites in the same orientation separated by one base pair.
18
HNF4
CAAAGTCCA
HNF4A and HNF4G are nuclear receptors that bind DNA only as homodimers, on a DR1: two hexameric half-sites in the same orientation separated by exactly one base pair.
11
ROR
AWNTAGGTCA
RORA, RORB and RORC (RORalpha/beta/gamma) are nuclear receptors that bind DNA as monomers to the ROR response element, or RORE: an AGGTCA nuclear-receptor half-site preceded by a 5-6 bp AT-rich extension, most often written AAAGTAGGTCA.
11
NR2E (TLX / PNR)
AAGTCA
NR2E is a small orphan nuclear-receptor group with two human members: NR2E1 (TLX, the homolog of Drosophila tailless) and NR2E3 (PNR, photoreceptor-specific nuclear receptor).
10
Estrogen-related receptors
TNAAGGTCA
The estrogen-related receptors ERRalpha (ESRRA), ERRbeta (ESRRB) and ERRgamma (ESRRG) are orphan nuclear receptors with no established natural ligand; their activity is set by coactivators such as PGC-1alpha rather than by a hormone.
10
NR4A (NUR77/NURR1)
AAAGGTCA
NR4A1 (NUR77), NR4A2 (NURR1) and NR4A3 (NOR-1) are orphan nuclear receptors and immediate-early genes: they are transcribed within minutes of serum stimulation, depolarization or antigen-receptor signaling and their proteins turn over quickly.
10
REV-ERB (NR1D)
AGGTCANNAGGTCA
REV-ERBalpha (NR1D1) and REV-ERBbeta (NR1D2) are nuclear receptors that lack the helix-12 activation surface and act only as repressors, recruiting the NCoR-HDAC3 complex and binding heme as a ligand.
9
Estrogen receptors
AGGTCAcvnTGnCCt
The estrogen receptors ERalpha (ESR1) and ERbeta (ESR2) are estradiol-activated nuclear receptors that bind DNA as homodimers on the estrogen response element, a 15 bp inverted repeat of the hexamer AGGTCA with a 3 bp spacer: AGGTCAnnnTGACCT, usually quoted as its 13 bp core GGTCAnnnTGACC.
6
NR5A (SF-1 / LRH-1)
TCAAGGTCA
NR5A1 (steroidogenic factor 1, SF-1) and NR5A2 (liver receptor homolog 1, LRH-1) are the mammalian relatives of Drosophila FTZ-F1.
6
NR6A1 (GCNF)
AGGTCAAGGTCA
NR6A1, better known as germ cell nuclear factor (GCNF), is the only mammalian member of nuclear receptor subfamily 6: one gene with no paralogue.

bZIP

8 families · 231 motifs
77
AP-1 (FOS/JUN)
TGASTCA
AP-1 is the collective name for dimers of the JUN proteins (JUN, JUNB, JUND) with the FOS proteins (FOS, FOSB, FOSL1, FOSL2), together with the related basic region-leucine zipper partners ATF3, JDP2 and BATF/BATF2/BATF3.
34
MAF (MARE)
TGCTGACTCAGCA
Maf proteins are basic region-leucine zipper factors that recognise an unusually long site, the Maf recognition element or MARE: 13 base pairs as TGCTGACTCAGCA, or 14 as TGCTGACGTCAGCA.
31
CREB / ATF (CRE)
TGACGTCA
The CREB/ATF group contains the basic region-leucine zipper factors CREB1, CREM, ATF1, ATF2, ATF7, ATF4 and CREB5.
26
ATF6 / CREB3 (ER stress)
TGACGTGG
This group collects the endoplasmic-reticulum-tethered basic region-leucine zipper factors ATF6 and ATF6B together with the CREB3 (OASIS/Luman) family - CREB3, CREB3L1, CREB3L2, CREB3L3 and CREB3L4 - and XBP1.
25
C/EBP
TTGCGCAA
The C/EBP family - CEBPA, CEBPB (NF-IL6), CEBPD, CEBPE, CEBPG, with DDIT3 (CHOP) as a heterodimer partner - binds the palindromic element TT(G/A)CGCAA, most often written as the 10-mer ATTGCGCAAT.
21
NFE2 / NRF / BACH (ARE)
TGACTCAGCA
This family covers the cap-n-collar (CNC) basic region-leucine zipper activators NFE2, NFE2L1 (NRF1) and NFE2L2 (NRF2) together with the BTB-bZIP repressors BACH1 and BACH2.
15
PAR bZIP (HLF/NFIL3/DBP)
TTACGTAA
The PAR bZIP group contains three proline- and acidic-amino-acid-rich basic region-leucine zipper activators - DBP (albumin D-site binding protein), HLF (hepatic leukemia factor) and TEF - together with NFIL3 (E4BP4), which lacks the PAR domain, represses rather than activates, and yet reads the same site.
2
Other bZIP
aaACGTak
This is not a family.

bHLH

13 families · 227 motifs
82
NeuroD / Atonal / ASCL
CAGATG
Class II basic helix-loop-helix (bHLH) proteins of the Atonal, achaete-scute, Olig and NSCL groups — NEUROD1/2, NEUROG1-3, ATOH1/7/8, ASCL1/2, OLIG1-3, PTF1A, BHLHA15, FIGLA, MSGN1, NHLH1/2 and relatives — bind DNA only as heterodimers with the broadly expressed class I E-proteins TCF3, TCF4 and TCF12.
30
MYC / MAX / MXD
CACGTG
MYC, MYCN and their obligate partner MAX bind the canonical E-box CACGTG as bHLH-LZ heterodimers, and the same site is bound by MAX homodimers and by the MAX-associated repressors MXD1-4, MXI1, MNT and MGA, which recruit Sin3-HDAC complexes.
26
TWIST / HAND
CAGATG
TWIST1/2, HAND1/2, TCF21, SCX and MESP1/2 are class II basic helix-loop-helix factors of mesoderm and neural crest.
17
Myogenic bHLH (MyoD)
CAGCTG
The four myogenic regulatory factors — MYOD1, MYF5, MYF6 (MRF4) and MYOG — plus the related repressor MSC (musculin/MyoR) are class II basic helix-loop-helix proteins restricted to the skeletal muscle lineage.
14
MITF / TFE (CLEAR)
GTCACGTGAC
MITF, TFE3, TFEB and TFEC are bHLH-LZ factors that dimerize only with each other, because a three-residue insertion kinks their leucine zipper.
13
E-proteins (TCF3/4/12)
CACCTG
TCF3 (E2A/E12/E47), TCF4 (E2-2) and TCF12 (HEB) are the broadly expressed class I bHLH proteins that serve as the general dimerization partners for tissue-restricted bHLH factors - MYOD in muscle, ASCL and NEUROD in neurons, TWIST in mesenchyme, TAL1 in blood - and are sequestered by ID proteins.
12
SREBP
TCACNCCAC
SREBP-1 and SREBP-2 are bHLH-LZ factors made as ER membrane precursors and activated by sterol-regulated proteolysis, so only the cleaved nuclear fragment binds DNA.
8
USF
GTCACGTGAC
USF1 and USF2 are ubiquitously expressed bHLH-LZ proteins, first purified as the adenovirus major late transcription factor (MLTF), that bind DNA as homodimers and heterodimers.
7
TAL1 / LYL1 (hematopoietic)
CAGNTG
TAL1 (SCL), LYL1 and TAL2 are haematopoietic and endothelial class II basic helix-loop-helix proteins with no intrinsic DNA-binding activity: they bind only as heterodimers with the class I E-proteins E12/E47, TCF4 or TCF12.
7
BHLHE40 / BHLHE41 (DEC1/2)
CACGTG
BHLHE40 and BHLHE41 - also known as DEC1/STRA13/SHARP-2 and DEC2/SHARP-1 - are bHLH repressors without a leucine zipper that bind the class-B E-box CACGTG and shut down transcription, both by competing for E-boxes with activating dimers such as CLOCK-BMAL1 and by recruiting histone deacetylases without contacting DNA.
6
TFAP4 (AP-4)
CAGCTG
TFAP4 (AP-4) is a single-gene bHLH-LZ family with no close paralogue.
3
Other bHLH
CACGTG
A residual bucket rather than a real family: it holds bHLH motifs that could not be placed in any of the defined bHLH families.
2
SPZ1
AGGGTAACAGC
SPZ1 is a single-gene family: one bHLH-Zip protein, with a basic helix-loop-helix domain followed by a leucine zipper, the same architecture as MYC, USF and the SREBPs.

Forkhead

2 families · 135 motifs
106
Forkhead (FOX)
RYAAAYA
Forkhead box (FOX) proteins are a family of about 50 human transcription factors that bind DNA as monomers through a ~100-residue winged-helix domain, named for the two loops, or wings, that flank its three-helix core.
29
Divergent forkhead sites (FOXP dimeric / FHL)
GTAAACA
This entry collects the forkhead factors whose preferred site is not the ordinary RYAAAYA element.

ETS

4 families · 134 motifs
81
ETS class I (ETS1/ERG/FLI1)
ACCGGAAGT
ETS proteins are a family of 28 human transcription factors that each bind DNA through a single ~85-residue winged helix-turn-helix domain and read a nine-base site whose informative part is the four-base core GGA(A/T).
25
ETS epithelial (ELF/EHF)
ACCCGGAAGT
ELF1, ELF2, ELF3, ELF4, ELF5 and EHF are the ELF branch of the ETS family.
16
ETV2 / ETV6-type
ACCGGAAGT
ETV2 (ER71), ETV6 (TEL) and ETV7 (TEL2) are ETS-domain proteins that read the same GGA(A/T) core as the rest of the family.
12
SPI1 / SPIB / SPIC (PU.1)
AAAGAGGAAGTG
SPI1 (PU.1), SPIB and SPIC are the class III branch of the ETS family.

Sox

5 families · 111 motifs
87
SOX (HMG box)
AACAAT
SOX proteins are the 20 human transcription factors built around a single SRY-type HMG box, a 78-residue L-shaped domain that binds DNA entirely in the minor groove, wedges a hydrophobic residue between base pairs and bends the double helix by 70-80 degrees.
18
TCF/LEF (HMG box)
CTTTGWW
TCF/LEF proteins are the DNA-binding end of the canonical Wnt pathway.
4
Other HMG-box
TGAACrvcGTTCA
This entry holds the HMG-box factors that are neither SOX nor TCF/LEF: HMG20A (iBRAF), HMG20B (BRAF35) and BBX (bobby sox homolog).
1
CIC (capicua)
TGAATGAA
CIC (capicua) is a single HMG-box repressor and the transcriptional sensor of ERK/MAPK signaling.
1
HBP1
TTCATTCATTCA
HBP1 is a single HMG-box transcriptional repressor and cell-cycle inhibitor, identified as a target of the retinoblastoma protein family.

POU

1 family · 82 motifs
82
POU (octamer)
ATGCAAAT
The octamer ATGCAAAT is the site read by the 16 human POU-domain factors, including OCT1/POU2F1, OCT2/POU2F2, PIT1/POU1F1, the BRN2/BRN1 group (POU3F1-4), the BRN3 group (POU4F1-3) and OCT4/POU5F1.

TALE homeodomain

2 families · 79 motifs
62
TALE homeodomain (PBX/MEIS/TGIF)
TGACAG
TALE homeodomain factors - PBX1-4, MEIS1-3, PKNOX1/2 (PREP1/2) and TGIF1/2 with the TGIF2LX/TGIF2LY retrogenes - carry a homeodomain with three extra residues inserted between helices 1 and 2, the Three Amino acid Loop Extension that names the class.
17
IRX (TALE, Iroquois)
ACATGT
IRX1 through IRX6, with the related factor MKX (Mohawk), form the Iroquois branch of the TALE homeodomain superclass - homeodomains carrying three extra residues between helices 1 and 2.

T-box

1 family · 60 motifs
60
T-box
AGGTGTGA
T-box sites are read by the seventeen human T-box proteins - TBXT (Brachyury), TBX1 to TBX6, TBX10, TBX15, TBX18 to TBX22, TBR1, EOMES and MGA - through a ~180-residue T domain that inserts a helix deep into a widened minor groove, a recognition mode found in no other family.

Rel

3 families · 55 motifs
29
NFAT
TGGAAA
NFAT sites are read by five proteins with a Rel-homology DNA-binding domain: the calcineurin-regulated NFATC1, NFATC2, NFATC3 and NFATC4, plus the structurally distinct, calcium-independent NFAT5 (TonEBP).
16
NF-kB / Rel
GGGRNNYYCC
The kB site is the element read by the five mammalian Rel/NF-kB proteins: NFKB1 (p105/p50), NFKB2 (p100/p52), RELA (p65), RELB and REL (c-Rel).
10
EBF / COE
TCCCNNGGGA
EBF1-EBF4 (COE1-COE4, also Olf-1 and O/E-1 to O/E-3) bind a 10-base palindrome, TCCCNNGGGA, as homodimers.

Paired box

1 family · 49 motifs
49
PAX paired domain
GTCACGC(A/T)TGA
The paired domain is a bipartite DNA-binding domain, unique to the nine human PAX proteins, that reads an unusually long site: a GTCACGC(A/T)TGA core set inside a footprint of roughly 15 to 20 base pairs.

IRF

1 family · 40 motifs
40
IRF
AANTGAAA
The nine human interferon regulatory factors, IRF1 through IRF9, bind DNA with an N-terminal winged helix-turn-helix domain studded with five conserved tryptophans.

Other

5 families · 39 motifs
20
Chromatin regulators without a classical DBD
cTATAGGtG
A deliberate holding bucket, and the place to learn why a ChIP-derived motif may not belong to the protein it is labelled with.
11
Thinly characterized small families
CACTCAc
This is not a motif family.
4
NRF1
GCGCATGCGC
NRF1 (nuclear respiratory factor 1, also alpha-PAL) is a single-gene family whose DNA-binding domain belongs to no common fold class, its closest relatives being sea urchin P3A2 and Drosophila Erect wing.
3
Other / unclassified
CnAAa
This is not a motif family.
1
PURA / PURB
GGNNGAGGGAGARRRR
PURA and PURB (Pur-alpha and Pur-beta) are PUR-repeat proteins that bind purine-rich DNA and RNA, with a strong preference for single strands rather than duplex.

bHLH-PAS

4 families · 39 motifs
19
HIF / ARNT
RCGTG
The hypoxia response element is the site read by HIF, a heterodimer of an oxygen-labile alpha subunit (HIF-1alpha, HIF-2alpha/EPAS1, HIF-3alpha) and the constitutive beta subunit ARNT (HIF-1beta) or its paralogue ARNT2.
12
CLOCK / BMAL1
CACGTG
CLOCK, BMAL1 (gene symbol ARNTL) and NPAS2 are basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) transcription factors that form the activating limb of the mammalian circadian clock.
5
AHR / AHRR
TNGCGTG
The xenobiotic response element is the site bound by the aryl hydrocarbon receptor, AHR, paired with ARNT.
3
NPAS3 / NPAS4 / other PAS
TCGTGa
NPAS3 and NPAS4 are neuronal bHLH-PAS transcription factors, relatives of CLOCK, HIF and AHR that heterodimerize with the same shared beta subunits ARNT and ARNT2 and read E-box-like sites built around a CGTG core.

E2F

1 family · 37 motifs
37
E2F / DP
TTTSSCGC
E2F factors are the transcriptional output of the retinoblastoma (RB) pathway and set the G1/S transition.

CUT homeodomain

2 families · 36 motifs
18
CUX (CUT homeodomain)
ATCGAT
CUX1, CUX2 and the SATB proteins SATB1 and SATB2 bind DNA with two kinds of domain at once: CUT repeats, each an independent ~70-residue DNA-binding module, plus a homeodomain.
18
ONECUT (HNF6)
TATTGATTT
ONECUT1 (HNF6), ONECUT2 and ONECUT3 bind DNA with a single CUT domain joined to a divergent homeodomain, and the two modules together read TATTGATT, often followed by a run of T.

GATA

1 family · 31 motifs
31
GATA
WGATAA
GATA factors are zinc-finger transcription factors that bind the six-base core WGATAA (usually AGATAA or TGATAA) through a single C4-type zinc finger plus a basic tail.

RFX

1 family · 31 motifs
31
RFX
GTTRCC(N0-3)RGYAAC
RFX proteins recognize the X-box, a pseudo-palindrome built from two GTTRCC-like half-sites separated by zero to three bases.

Myb/SANT

3 families · 29 motifs
22
MYB / MYB-like
YAACKG
MYB factors bind the Myb binding site (MBS), a six-base element written YAACKG, through two or three imperfect ~52-residue repeats that each fold into a helix-turn-helix-like unit.
5
Telobox (TERF1/TERF2/ZBTB48)
TTAGGG
The telobox factors TERF1 (TRF1) and TERF2 (TRF2) bind the vertebrate telomeric repeat TTAGGG through a single Myb-type helix-turn-helix domain that is, structurally, a homeodomain-like fold.
2
CDC5L
gCGCTGAGc
CDC5L is the human orthologue of fission yeast Cdc5, a protein with two N-terminal Myb/SANT-like repeats whose main established job is not transcription at all: it is an essential component of the spliceosomal Prp19/CDC5L complex required for the second catalytic step of pre-mRNA splicing, and it is visible in cryo-EM structures of the human spliceosome.

bHLH-Orange

1 family · 26 motifs
26
HES / HEY (N-box)
CACGYG
HES1-7, HEY1/2, HEYL and HELT are the vertebrate hairy/Enhancer-of-split relatives: bHLH repressors with an Orange domain that sets partner choice and a C-terminal WRPW or YRPW peptide that recruits TLE/Groucho corepressors.

STAT

1 family · 26 motifs
26
STAT
TTCNNNGAA
The seven human STAT proteins - STAT1, STAT2, STAT3, STAT4, STAT5A, STAT5B and STAT6 - sit latent in the cytoplasm until a receptor-associated JAK kinase phosphorylates a single C-terminal tyrosine.

HSF

1 family · 24 motifs
24
HSF
TTCTAGAAcdTTC
Heat shock factors bind the heat shock element (HSE), an array of the 5-base unit nGAAn in alternating orientation: nTTCn-nGAAn-nTTCn and longer runs.

Grainyhead

1 family · 23 motifs
23
Grainyhead (GRHL)
AACCGGTT
The Grainyhead/CP2 family binds the palindrome AACCGGTT through an immunoglobulin-like DNA-binding domain that shares a fold with p53 but differs from it in important details.

AP-2

1 family · 22 motifs
22
AP-2 (TFAP2)
GCC(N3)GGC
The five human TFAP2 proteins (TFAP2A-E, historically AP-2 alpha through epsilon) bind a pseudo-palindrome made of GCC and GGC triplets separated by exactly three bases.

MADS

2 families · 22 motifs
18
MEF2
CTA(A/T)4TAG
MEF2 sites are bound by the four MADS-box factors MEF2A, MEF2B, MEF2C and MEF2D, which act as obligate dimers.
4
SRF
CCW6GG
The CArG box is the site of a single protein, serum response factor, which binds as a homodimer through a MADS box - the same fold MEF2 uses, reading a different sequence.

SMAD/NF-1

1 family · 21 motifs
21
NFI (CTF/NF-1)
TTGGC(N5)GCCAA
Nuclear factor I proteins bind a 15-bp palindrome, TTGGC followed by five variable bases and GCCAA.

MBD/CxxC

1 family · 21 motifs
21
MBD and CxxC readers
CG
This family puts two opposite kinds of reader in one place.

SIX homeodomain

1 family · 21 motifs
21
SIX
TGATAC
The six human SIX genes encode homeodomain proteins with an additional SIX domain that recruits the EYA family of transcriptional coactivators.

SMAD

1 family · 20 motifs
20
SMAD
CtAGACa
SMAD proteins are the intracellular effectors of TGF-beta family signaling.

DM

1 family · 20 motifs
20
DMRT (DM domain)
ACAWTGTW
DMRT proteins are the DM-domain transcription factors, named after Drosophila Doublesex and C.

TEA

1 family · 17 motifs
17
TEAD
GGAATG
The four human TEAD proteins (TEAD1-4, formerly TEF-1, TEF-4, TEF-5 and TEF-3) bind the MCAT element GGAATG, read on the other strand as CATTCC.

Runt

1 family · 16 motifs
16
RUNX
TGYGGT
RUNX sites are read by RUNX1, RUNX2 and RUNX3 through the Runt domain, a 128-residue immunoglobulin-like fold in the same structural class as NF-kB and p53.

CENPB/pogo

1 family · 16 motifs
16
CENP-B / pogo / Tigger
TTCGTTGGAA
The third and largest of the atlas's domesticated-transposase families.

SAND

1 family · 15 motifs
15
SAND domain (AIRE/SP100/GMEB)
ACGY-N(1-9)-RCGY
The SAND domain is a small DNA-binding fold named after the four proteins in which it was first recognized: Sp100, AIRE, NucP41/75 and DEAF1.

p53

1 family · 13 motifs
13
p53 family
RRRCWWGYYY(N)0-13RRRCWWGYYY
The p53 response element is bound by three paralogues - TP53, TP63 and TP73 - through a shared, structurally unusual DNA-binding domain that works only as a tetramer.

CBF/NF-Y

1 family · 9 motifs
9
NF-Y (CBF)
CCAAT
NF-Y is a heterotrimer of NFYA, NFYB and NFYC that binds the CCAAT box, one of the most frequent elements in eukaryotic promoters.

BED_ZF

1 family · 9 motifs
9
BED-type zinc finger
TATCGCGACAT
BED fingers are zinc-coordinating DNA-binding modules named for the two proteins in which they were first recognized, Drosophila BEAF and DREF, and they are shared with the hAT superfamily of DNA transposases.

POU-homeodomain hybrid

1 family · 9 motifs
9
HNF1
GTTAATNATTAAC
HNF1A and HNF1B are the only two members of this family, and they bind an unusually long 13-bp near-palindrome, GTTAATNATTAAC, as an obligate dimer.

ARID

1 family · 8 motifs
8
ARID / BRIGHT
ATTAAT
ARID stands for AT-rich interaction domain, and this family is restricted to the four human ARID proteins that really do read AT-rich sequence: ARID3A (Bright), ARID3B, ARID5A and ARID5B.

GCM

1 family · 8 motifs
8
GCM (glial cells missing)
ATRCGGGT
GCM1 and GCM2 (glial cells missing 1 and 2) are the only human members of a small metazoan family that binds DNA through the GCM domain, a conserved 150-residue region with a fold unlike any other transcription factor class: two subdomains held together by structural zinc ions, reading the major groove with a five-stranded beta-sheet rather than an alpha-helix.

RNA-binding

1 family · 8 motifs
8
RNA-binding proteins with inferred DNA motifs
aATAAAA
This is not a motif family.

DACH/SKI

1 family · 7 motifs
7
DACH / SKI-family corepressors
TTAATTAC
These are transcriptional corepressors, not classical sequence-specific activators.

THAP finger

1 family · 6 motifs
6
THAP-type zinc finger
GCAGGGCA
THAP-type zinc fingers are C2CH modules whose closest known relative is the site-specific DNA-binding domain of the Drosophila P-element transposase, making this a family of domesticated transposase DNA-binding domains.

TBP

1 family · 5 motifs
5
TBP / TATA
TATAWAWR
The TATA box is the oldest known eukaryotic core promoter element and the binding site of TBP, the TATA-box-binding protein.

CSL

1 family · 4 motifs
4
CSL / RBPJ
GTGGGAA
CSL is the DNA-binding transcription factor at the end of the Notch pathway, named for its three orthologues: CBF1/RBPJ in mammals, Suppressor of Hairless in Drosophila and LAG-1 in C.

Prospero

1 family · 4 motifs
4
PROX1 (Prospero)
TAAGACG
PROX1 is the human counterpart of Drosophila Prospero, and it binds DNA with a module unlike any other homeodomain: a highly divergent homeodomain fused to a conserved Prospero domain, the two folding into one structural unit called the homeo-prospero domain.

Ndt80/PhoG

1 family · 3 motifs
3
Ndt80/PhoG-like (C11orf9/MYRF)
TGGTACCA
This family is named after the budding yeast meiotic activator Ndt80, whose DNA-binding domain defines an immunoglobulin-like fold shared by the human proteins MYRF and MYRFL.

HMGA

1 family · 3 motifs
3
HMGA (AT-hook)
ATTTTTA
HMGA1 and HMGA2 have no sequence specificity worth scanning for.

CSD

1 family · 3 motifs
3
Cold-shock domain (YBX)
GATGGTAC
A one-protein family.

CCHC zinc finger

1 family · 3 motifs
3
MYT1 / ST18 (CCHC zinc finger)
AAAGTTT
MYT1, MYT1L and ST18 are the three human members of the MYT/NZF family, which uses an unusual non-classical zinc finger (described as C2HC or CCHHC, not the C2H2 fold of most zinc-finger transcription factors) arranged in two widely separated clusters of fingers.

CG-1

1 family · 2 motifs
2
CAMTA
YGCANTGCG
CAMTA1 and CAMTA2 (calmodulin-binding transcription activators) are the two human members of a family defined by the CG-1 domain, an N-terminal DNA-binding module unrelated to any other class, followed by a TIG domain, ankyrin repeats and calmodulin-binding IQ motifs.

CRC/tesmin

1 family · 2 motifs
2
LIN54 / DREAM (CHR)
TTYGAA
LIN54 is the DNA-binding subunit of the MuvB core, the module shared by the repressive DREAM complex and the activating MMB (B-MYB-MuvB) and FOXM1-MuvB complexes.
how this page was made Drafted by a language model reading the primary literature, then checked: every cited PMID is resolved against PubMed and its citation text regenerated from PubMed's own record, and every claim about the motifs themselves is checked against the matrices in the four source databases. Methods and limits →