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PR01282

Identifier
COUPTNFACTOR  [View Relations]  [View Alignment]  
Accession
PR01282
No. of Motifs
9
Creation Date
20-FEB-2000
Title
COUP transcription factor (2F nuclear receptor) family signature
Database References
PRINTS; PR00398 STRDHORMONER
Literature References
1. NUCLEAR RECEPTORS NOMENCLATURE COMMITTEE
A unified nomenclature system for the nuclear receptor superfamily.
CELL 97 161-163 (1999).
 
2. NISHIKAWA, J-I., KITAURA, M., IMAGAWA, M. AND NISHIHARA, T.
Vitamin D receptor contains multiple dimerisation interfaces that
are functionally different.
NUCLEIC ACIDS RES. 23(4) 606-611 (1995).
 
3. DE VOS, P., SCHMITT, J., VERHOEVEN, G. AND STUNNENBERG, G.
Human androgen receptor expressed in HeLa cells activates transcription
in vitro.
NUCLEIC ACIDS RES. 22(7) 1161-1166 (1994).
 
4. QIU, Y., COONEY, A.J., KURATANI, S., DEMAYO, F.J., TSAI, S.Y.
AND TSAI, M.J.
Spatiotemporal expression patterns of chicken ovalbumin upstream 
promoter-transcription factors in the developing mouse central nervous
system: evidence for a role in segmental patterning of the diencephalon.
PROC.NATL.ACAD.SCI.U.S.A. 91 4451-4455 (1994). 
 
5. JONK, L.J., DE JONGE, M.E., PALS, C.E., WISSINK S., VERVAART, J.M.,
SCHOORLEMMER, J. AND KRUIJER, W.
Cloning and expression during development of three murine members of the
COUP family of nuclear orphan receptors.
MECH.DEV. 47 81-97 (1994). 

Documentation
Steroid or nuclear hormone receptors (NRs) constitute an important super-
family of transcription regulators that are involved in widely diverse 
physiological functions, including control of embryonic development, cell
differentiation and homeostasis [1]. Members of the superfamily include the
steroid hormone receptors and receptors for thyroid hormone, retinoids, 
1,25-dihydroxy-vitamin D3 and a variety of other ligands. The proteins 
function as dimeric molecules in nuclei to regulate the transcription of 
target genes in a ligand-responsive manner [2,3]. In addition to C-terminal
ligand-binding domains, these nuclear receptors contain a highly-conserved,
N-terminal zinc-finger that mediates specific binding to target DNA 
sequences, termed ligand-responsive elements. In the absence of ligand,
steroid hormone receptors are thought to be weakly associated with nuclear
components; hormone binding greatly increases receptor affinity.
 
NRs are extremely important in medical research, a large number of them
being implicated in diseases such as cancer, diabetes, hormone resistance
syndromes, etc. [1]. While several NRs act as ligand-inducible transcription
factors, many do not yet have a defined ligand and are accordingly termed 
"orphan" receptors. During the last decade, more than 300 NRs have been
described, many of which are orphans, which cannot easily be named due to 
current nomenclature confusions in the literature. However, a new system 
has recently been introduced in an attempt to rationalise the increasingly 
complex set of names used to describe superfamily members [1].
 
Chicken ovalbumin upstream promoter-transcription factor (COUP-TF) genes
encode transcription factors that belong to the orphan group of the
steroid/thyroid hormone receptor superfamily [4]. COUP-TF binds to the
ovalbumin promoter and, in conjunction with the S300-II protein, stimulates
initiation of transcription. The protein binds to both direct repeats and
palindromes of the 5'-AGGTCA-3' motif.
 
Murine homologues of members of the COUP-TF family, COUP-TF1, ARP-1 and 
EAR2, have been isolated and shown to be highly similar to their human
counterparts [5]. Although these three genes appear to be expressed in
tissues derived from all three germ layers, COUP-TF1 and ARP-1 have been
found to be expressed predominantly in the developing central nervous 
system in mutually exclusive domains [5]. Strong ARP-1 expression has
also been detected in lung and kidney [5]. Results from such studies
suggest an important role for the members of the COUP-TF family in the 
hormonal control of gene expression regulating embryogenesis, and in the
development and differentiation of the CNS, including the specification
of diencephalic neuromeres [4].
 
COUPTNFACTOR is a 9-element fingerprint that provides a signature for 
the COUP-related transcription factor family. The fingeprint was derived
from an initial alignment of 7 sequences: the motifs were drawn from 
conserved regions spanning virtually the full alignment length, focusing on
those sections that characterise the COUP-related nuclear receptors but
distinguish them from the rest of the steroid hormone receptor superfamily
- motifs 1-8 span the putative ligand-binding domain; and motifs 7-9 reside
within the putative dimerisation domain. Two iterations on SPTR37_10f were
required to reach convergence, at which point a true set comprising 15 
sequences was identified. Several partial matches were also found: 
7UP2_DROME is a Drosophila seven-up type 2 steroid receptor that fails to
match the C-terminal motifs; O96680 and Q9YGL3 are related sequences that
match only 2 motifs.
Summary Information
  15 codes involving  9 elements
0 codes involving 8 elements
0 codes involving 7 elements
0 codes involving 6 elements
1 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
2 codes involving 2 elements
Composite Feature Index
9151515151515151515
8000000000
7000000000
6000000000
5111110000
4000000000
3000000000
2001000210
123456789
True Positives
7UP1_DROME    ARP1_CHICK    ARP1_HUMAN    ARP1_MOUSE    
ARP1_RAT COT1_MOUSE COTF_HUMAN EAR2_HUMAN
EAR2_MOUSE O09017 Q06725 Q06726
Q62681 Q91430 Q91720
True Positive Partials
Codes involving 5 elements
7UP2_DROME
Codes involving 2 elements
O96680 Q9YGL3
Sequence Titles
7UP1_DROME  STEROID RECEPTOR SEVEN-UP TYPE 1 - DROSOPHILA MELANOGASTER (FRUIT FLY). 
ARP1_CHICK TRANSCRIPTION FACTOR COUP 2 (COUP-TF II) - GALLUS GALLUS (CHICKEN).
ARP1_HUMAN APOLIPOPROTEIN AI REGULATORY PROTEIN-1 (ARP-1) (TRANSCRIPTION FACTOR COUP 2) (CO
ARP1_MOUSE APOLIPOPROTEIN AI REGULATORY PROTEIN-1 (ARP-1) (TRANSCRIPTION FACTOR COUP 2) (CO
ARP1_RAT APOLIPOPROTEIN AI REGULATORY PROTEIN-1 (ARP-1) (TRANSCRIPTION FACTOR COUP 2) (CO
COT1_MOUSE COUP TRANSCRIPTION FACTOR 1 (COUP-TF1) (COUP-TFI) - MUS MUSCULUS (MOUSE).
COTF_HUMAN COUP TRANSCRIPTION FACTOR (COUP-TF) (V-ERBA RELATED PROTEIN EAR-3) - HOMO SAPIEN
EAR2_HUMAN V-ERBA RELATED PROTEIN EAR-2 - HOMO SAPIENS (HUMAN).
EAR2_MOUSE V-ERBA RELATED PROTEIN EAR-2 - MUS MUSCULUS (MOUSE).
O09017 OVALBUMIN UPSTREAM PROMOTER GAMMA NUCLEAR RECEPTOR RCOUPG - RATTUS NORVEGICUS (R
Q06725 STEROID RECEPTOR HOMOLOG SVP 44 - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
Q06726 STEROID RECEPTOR HOMOLOG SVP 46 - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
Q62681 ORPHAN RECEPTOR COUP-TFI (HCOUP-TF1 HOMOLOG) - RATTUS NORVEGICUS (RAT).
Q91430 SVP[40]=SVP-RELATED NUCLEAR RECEPTOR/RETINOID SIGNALING MODULATOR - BRACHYDANIO
Q91720 COUP TRANSCRIPTION FACTOR - XENOPUS LAEVIS (AFRICAN CLAWED FROG).

7UP2_DROME STEROID RECEPTOR SEVEN-UP TYPE 2 - DROSOPHILA MELANOGASTER (FRUIT FLY).

O96680 DISSATISFACTION - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q9YGL3 TAILLESS - ORYZIAS LATIPES (MEDAKA FISH).
Scan History
SPTR37_10f 2  50   NSINGLE    
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
EAVQRGRMPPTQP COT1_MOUSE 153 153 -
EAVQRGRMPPTQP COTF_HUMAN 154 154 -
EAVQRGRMPPTQP ARP1_HUMAN 147 147 -
EAVQRGRMPPTQP ARP1_MOUSE 147 147 -
EAVQRGRVPPTQP 7UP1_DROME 268 268 -
EAVQRGRIPHSLP EAR2_HUMAN 124 124 -
EAVQRGRIPHALP EAR2_MOUSE 125 125 -

Motif 2 width=16
Element Seqn Id St Int Rpt
LSGYISLLLRAEPYPT COT1_MOUSE 184 18 -
LSGYISLLLRAEPYPT COTF_HUMAN 185 18 -
LSGYISLLLRAEPYPT ARP1_HUMAN 178 18 -
LSGYISLLLRAEPYPT ARP1_MOUSE 178 18 -
LSSYISLLLRAEPYPT 7UP1_DROME 308 27 -
VSELIAQLLRAEPYPA EAR2_HUMAN 166 29 -
VSELIAQLLRAEPYPA EAR2_MOUSE 158 20 -

Motif 3 width=17
Element Seqn Id St Int Rpt
GIENICELAARLLFSAV COT1_MOUSE 214 14 -
GIENICELAARLLFSAV COTF_HUMAN 215 14 -
GIENICELAARMLFSAV ARP1_HUMAN 208 14 -
GIENICELAARMLFSAV ARP1_MOUSE 208 14 -
GIDNICELAARLLFSAV 7UP1_DROME 337 13 -
GIDNVCELAARLLFSTV EAR2_HUMAN 198 16 -
GIDNVCELAARLLFSTV EAR2_MOUSE 185 11 -

Motif 4 width=19
Element Seqn Id St Int Rpt
MPLHVAPLLAAAGLHASPM COT1_MOUSE 268 37 -
MPLHVAPLLAAAGLHASPM COTF_HUMAN 269 37 -
MPLHVAPLLAAAGLHASPM ARP1_HUMAN 262 37 -
MPLHVAPLLAAAGLHASPM ARP1_MOUSE 262 37 -
MPLHVAPLLAAAGLHASPM 7UP1_DROME 391 37 -
LPLHTAPLLAAAGLHAAPM EAR2_HUMAN 251 36 -
LPLHTAPLLAAAGLHAAPM EAR2_MOUSE 239 37 -

Motif 5 width=15
Element Seqn Id St Int Rpt
ADRVVAFMDHIRIFQ COT1_MOUSE 288 1 -
ADRVVAFMDHIRIFQ COTF_HUMAN 289 1 -
ADRVVAFMDHIRIFQ ARP1_HUMAN 282 1 -
ADRVVAFMDHIRIFQ ARP1_MOUSE 282 1 -
ADRVVAFMDHIRIFQ 7UP1_DROME 411 1 -
AERAVAFMDQVRAFQ EAR2_HUMAN 271 1 -
AERAVAFMDQVRAFQ EAR2_MOUSE 259 1 -

Motif 6 width=13
Element Seqn Id St Int Rpt
FTSDACGLSDAAH COT1_MOUSE 327 24 -
FTSDACGLSDAAH COTF_HUMAN 328 24 -
FTSDACGLSDVAH ARP1_HUMAN 321 24 -
FTSDACGLSDVAH ARP1_MOUSE 321 24 -
FTTDACGLSDVTH 7UP1_DROME 450 24 -
FTPDACGLSDPAH EAR2_HUMAN 310 24 -
FTPDACGLSDPAH EAR2_MOUSE 298 24 -

Motif 7 width=14
Element Seqn Id St Int Rpt
PSLRTVSSSVIEQL COT1_MOUSE 374 34 -
PSLRTVSSSVIEQL COTF_HUMAN 375 34 -
PSLRTVSSSVIEQL ARP1_HUMAN 368 34 -
PSLRTVSSSVIEQL ARP1_MOUSE 368 34 -
PSLRTVSSQVIEQL 7UP1_DROME 497 34 -
PALRAVPASLISQL EAR2_HUMAN 357 34 -
PALRAVPASLISKL EAR2_MOUSE 345 34 -

Motif 8 width=12
Element Seqn Id St Int Rpt
GKTPIETLIRDM COT1_MOUSE 394 6 -
GKTPIETLIRDM COTF_HUMAN 395 6 -
GKTPIETLIRDM ARP1_HUMAN 388 6 -
GKTPIETLIRDM ARP1_MOUSE 388 6 -
GKTPIETLIRDM 7UP1_DROME 517 6 -
GKTPIETLIRDM EAR2_HUMAN 377 6 -
GKTPIETLIRDM EAR2_MOUSE 365 6 -

Motif 9 width=14
Element Seqn Id St Int Rpt
MLLSGSSFNWPYMS COT1_MOUSE 405 -1 -
MLLSGSSFNWPYMS COTF_HUMAN 406 -1 -
MLLSGSSFNWPYMA ARP1_HUMAN 399 -1 -
MLLSGSSFNWPYMA ARP1_MOUSE 399 -1 -
MLLSGNSFSWPYLP 7UP1_DROME 528 -1 -
MLLSGSTFNWPYGS EAR2_HUMAN 388 -1 -
MLLSGSTFNWPYGS EAR2_MOUSE 376 -1 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
EAVQRGRMPPTQP COT1_MOUSE 153 153 -
EAVQRGRMPPTQP Q06725 144 144 -
EAVQRGRMPPTQP COTF_HUMAN 154 154 -
EAVQRGRMPPTQP ARP1_CHICK 143 143 -
EAVQRGRMPPTQP Q91430 155 155 -
EAVQRGRMPPTQP ARP1_HUMAN 147 147 -
EAVQRGRMPPTQP ARP1_RAT 147 147 -
EAVQRGRMPPTQP ARP1_MOUSE 147 147 -
EAVQRGRMPPTQP Q62681 151 151 -
EAVQRGRVPPTQP 7UP1_DROME 268 268 -
EAVQRGRMSNSQS Q06726 122 122 -
REVQRGRMSHPQT Q91720 130 130 -
EAVQRGRIPHSLP EAR2_HUMAN 124 124 -
EAVQRGRIPHALP EAR2_MOUSE 125 125 -
EAVQPGPIPHALP O09017 125 125 -

Motif 2 width=16
Element Seqn Id St Int Rpt
LSGYISLLLRAEPYPT COT1_MOUSE 184 18 -
LSGYISLLLRAEPYPT Q06725 175 18 -
LSGYISLLLRAEPYPT COTF_HUMAN 185 18 -
LSGYISLLLRAEPYPT ARP1_CHICK 174 18 -
LSGYISLLLRAEPYPT Q91430 186 18 -
LSGYISLLLRAEPYPT ARP1_HUMAN 178 18 -
LSGYISLLLRAEPYPT ARP1_RAT 178 18 -
LSGYISLLLRAEPYPT ARP1_MOUSE 178 18 -
LSGYISLLLRAEPYPT Q62681 182 18 -
LSSYISLLLRAEPYPT 7UP1_DROME 308 27 -
LSGFISLLLRAEPYPT Q06726 153 18 -
LTGFISLLLRAEPYPT Q91720 161 18 -
VSELIAQLLRAEPYPA EAR2_HUMAN 166 29 -
VSELIAQLLRAEPYPA EAR2_MOUSE 158 20 -
VSELIAQLLRAEPYPA O09017 158 20 -

Motif 3 width=17
Element Seqn Id St Int Rpt
GIENICELAARLLFSAV COT1_MOUSE 214 14 -
GIENICELAARLLFSAV Q06725 205 14 -
GIENICELAARLLFSAV COTF_HUMAN 215 14 -
GIENICELAARMLFSAV ARP1_CHICK 204 14 -
GIENICELAARMLFSAV Q91430 216 14 -
GIENICELAARMLFSAV ARP1_HUMAN 208 14 -
GIENICELAARMLFSAV ARP1_RAT 208 14 -
GIENICELAARMLFSAV ARP1_MOUSE 208 14 -
GIENICELAARLLFSAV Q62681 212 14 -
GIDNICELAARLLFSAV 7UP1_DROME 337 13 -
GIENICELAARLLFSAV Q06726 183 14 -
GIENICELAARLLFSAI Q91720 191 14 -
GIDNVCELAARLLFSTV EAR2_HUMAN 198 16 -
GIDNVCELAARLLFSTV EAR2_MOUSE 185 11 -
GIDNVCELAARLLFSTV O09017 185 11 -

Motif 4 width=19
Element Seqn Id St Int Rpt
MPLHVAPLLAAAGLHASPM COT1_MOUSE 268 37 -
MPLHVAPLLAAAGLHASPM Q06725 259 37 -
MPLHVAPLLAAAGLHASPM COTF_HUMAN 269 37 -
MPLHVAPLLAAAGLHASPM ARP1_CHICK 258 37 -
MPLHVAPLLAAAGLHASPM Q91430 270 37 -
MPLHVAPLLAAAGLHASPM ARP1_HUMAN 262 37 -
MPLHVAPLLAAAGLHASPM ARP1_RAT 262 37 -
MPLHVAPLLAAAGLHASPM ARP1_MOUSE 262 37 -
SMPLHVAVLAAAGLHASPM Q62681 265 36 -
MPLHVAPLLAAAGLHASPM 7UP1_DROME 391 37 -
MPLHVAPLLAAAGLHASPM Q06726 237 37 -
MPLHVAPLLARAGLHASPM Q91720 245 37 -
LPLHTAPLLAAAGLHAAPM EAR2_HUMAN 251 36 -
LPLHTAPLLAAAGLHAAPM EAR2_MOUSE 239 37 -
VPLHTAPLLAAAGLHAGPM O09017 239 37 -

Motif 5 width=15
Element Seqn Id St Int Rpt
ADRVVAFMDHIRIFQ COT1_MOUSE 288 1 -
ADRVVAFMDHIRIFQ Q06725 279 1 -
ADRVVAFMDHIRIFQ COTF_HUMAN 289 1 -
ADRVVAFMDHIRIFQ ARP1_CHICK 278 1 -
ADRVVAFMDHIRIFQ Q91430 290 1 -
ADRVVAFMDHIRIFQ ARP1_HUMAN 282 1 -
ADRVVAFMDHIRIFQ ARP1_RAT 282 1 -
ADRVVAFMDHIRIFQ ARP1_MOUSE 282 1 -
ADRVVAFMDHIRIFQ Q62681 285 1 -
ADRVVAFMDHIRIFQ 7UP1_DROME 411 1 -
AERVVAFMDHIRVFQ Q06726 257 1 -
ADRVVAFMDHIRIFQ Q91720 265 1 -
AERAVAFMDQVRAFQ EAR2_HUMAN 271 1 -
AERAVAFMDQVRAFQ EAR2_MOUSE 259 1 -
AERAVAFMDQVRAFQ O09017 259 1 -

Motif 6 width=13
Element Seqn Id St Int Rpt
FTSDACGLSDAAH COT1_MOUSE 327 24 -
FTSDACGLSDAAH Q06725 318 24 -
FTSDACGLSDAAH COTF_HUMAN 328 24 -
FTSDACGLSDVAH ARP1_CHICK 317 24 -
FTSDACGLSDVAH Q91430 329 24 -
FTSDACGLSDVAH ARP1_HUMAN 321 24 -
FTSDACGLSDVAH ARP1_RAT 321 24 -
FTSDACGLSDVAH ARP1_MOUSE 321 24 -
FTSDACGLSDAAH Q62681 324 24 -
FTTDACGLSDVTH 7UP1_DROME 450 24 -
FTSDAMGLSDVAH Q06726 296 24 -
FTPDAVGLSDIGH Q91720 304 24 -
FTPDACGLSDPAH EAR2_HUMAN 310 24 -
FTPDACGLSDPAH EAR2_MOUSE 298 24 -
FTPDACGLSDPAH O09017 298 24 -

Motif 7 width=14
Element Seqn Id St Int Rpt
PSLRTVSSSVIEQL COT1_MOUSE 374 34 -
PSLRTVSSSVIEQL Q06725 365 34 -
PSLRTVSSSVIEQL COTF_HUMAN 375 34 -
PSLRTVSSSVIEQL ARP1_CHICK 364 34 -
PSLRTVSSSVIEQL Q91430 376 34 -
PSLRTVSSSVIEQL ARP1_HUMAN 368 34 -
PSLRTVSSSVIEQL ARP1_RAT 368 34 -
PSLRTVSSSVIEQL ARP1_MOUSE 368 34 -
PSLRTVSSSVIEQL Q62681 371 34 -
PSLRTVSSQVIEQL 7UP1_DROME 497 34 -
PSLRIVSSPVIEQL Q06726 343 34 -
PSLRIVSAPVIEQL Q91720 351 34 -
PALRAVPASLISQL EAR2_HUMAN 357 34 -
PALRAVPASLISKL EAR2_MOUSE 345 34 -
PALRAVPASLISQL O09017 345 34 -

Motif 8 width=12
Element Seqn Id St Int Rpt
GKTPIETLIRDM COT1_MOUSE 394 6 -
GKTPIETLIRDM Q06725 385 6 -
GKTPIETLIRDM COTF_HUMAN 395 6 -
GKTPIETLIRDM ARP1_CHICK 384 6 -
GKTPIETLIRDM Q91430 396 6 -
GKTPIETLIRDM ARP1_HUMAN 388 6 -
GKTPIETLIRDM ARP1_RAT 388 6 -
GKTPIETLIRDM ARP1_MOUSE 388 6 -
GKTPIETLIRDM Q62681 391 6 -
GKTPIETLIRDM 7UP1_DROME 517 6 -
GKTPIETLLRDM Q06726 363 6 -
GKTPIETLIRDM Q91720 371 6 -
GKTPIETLIRDM EAR2_HUMAN 377 6 -
GKTPIETLIRDM EAR2_MOUSE 365 6 -
GKTPIETLIRDM O09017 365 6 -

Motif 9 width=14
Element Seqn Id St Int Rpt
MLLSGSSFNWPYMS COT1_MOUSE 405 -1 -
MLLSGSSFNWPYMS Q06725 396 -1 -
MLLSGSSFNWPYMS COTF_HUMAN 406 -1 -
MLLSGSSFNWPYMS ARP1_CHICK 395 -1 -
MLLSGSSFNWPYMS Q91430 407 -1 -
MLLSGSSFNWPYMA ARP1_HUMAN 399 -1 -
MLLSGSSFNWPYMA ARP1_RAT 399 -1 -
MLLSGSSFNWPYMA ARP1_MOUSE 399 -1 -
MLLSGSSFNWPYMS Q62681 402 -1 -
MLLSGNSFSWPYLP 7UP1_DROME 528 -1 -
MLLSGSSYNWPYMP Q06726 374 -1 -
MLLSGSSFNWPYMP Q91720 382 -1 -
MLLSGSTFNWPYGS EAR2_HUMAN 388 -1 -
MLLSGSTFNWPYGS EAR2_MOUSE 376 -1 -
MLLSGSTFNWPYGS O09017 376 -1 -