WORKLIST ENTRIES (1):

RORNUCRECPTR View alignment View Structure    Nuclear receptor ROR family signature
 Type of fingerprint: COMPOUND with 5  elements
Links:
   PRINTS; PR00047 STROIDFINGER; PR00398 STRDHORMONER
   PRINTS; PR00521 ANDROGENR; PR01282 COUPTNFACTOR; PR01283 ECDYSTEROIDR
   PRINTS; PR00528 GLCORTICOIDR; PR01284 NUCLEARECPTR; PR00350 VITAMINDR
   PRINTS; PR00544 PROGESTRONER; PR01288 PROXISOMEPAR; PR00545 RETINOIDXR
   PRINTS; PR00543 OESTROGENR; PR00546 THYROIDHORMR; PR02034 LIVERXRECPTR
   PDB; 1K4W 3Dinfo; 1N4H 3Dinfo; 1N83 3Dinfo; 1NQ7 3Dinfo; 1S0X 3Dinfo
   SCOP; 1K4W; 1N4H; 1N83; 1NQ7; 1S0X
   CATH; 1K4W; 1N4H; 1N83; 1NQ7; 1S0X
   MIM; 600825; 601972; 602943

 Creation date 13-FEB-2000; UPDATE 09-JUL-2010

   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. GIGUERE, V., TINI, M., FLOCK, G., ONG, E., EVANS, R.M. AND OTULAKOWSKI, G.
   Isoform-specific amino-terminal domains dictate DNA-binding properties of
   ROR alpha, a novel family of orphan hormone nuclear receptors.
   GENES DEV. 8 538-553 (1994). 

   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].
  
   Three isoforms of a novel member of the steroid hormone nuclear receptor
   superfamily related to retinoic acid receptors have been identified [4].
   The isoforms (designated ROR alpha 1, ROR alpha 2 and ROR alpha 3) share
   common DNA- and putative ligand-binding domains but are characterised by
   distinct N-terminal domains generated by alternative RNA processing [4].
   These differences in the N-terminal domains result in differential DNA-
   binding activity for the different isoforms: ROR alpha 1 binds to and 
   constitutively activates transcription from a large subset of ROR elements,
   while ROR alpha 2 recognises ROR elements with strict specificity and 
   displays weaker transcriptional activity [4]. The N-terminal domain and
   zinc finger region work in concert to confer high affinity and specific 
   DNA-binding properties to the ROR isoforms and suggest a novel strategy 
   to control DNA-binding activity of nuclear receptors [4]. 
  
   RORNUCRECPTR is a 5-element fingerprint that provides a signature for the
   nuclear receptor ROR family. The fingerprint was derived from an initial
   alignment of 6 sequences: the motifs were drawn from conserved regions 
   spanning the C-terminal half of the alignment, focusing on those sections
   that characterise the ROR receptors but distinguish them from the rest of
   the steroid hormone receptor superfamily - motif 1 lies at the C-terminal
   extremity of the hinge region, and motifs 2-5 reside in the ligand-binding
   domain. Two iterations on SPTR37_10f were required to reach convergence,
   at which point a true set comprising 13 sequences was identified. Five
   partial matches were also found, all of which are related steroid hormone
   receptors.
  
   An update on SPTR57.15_40.15f identified a true set of 24 sequences, and 
   twelve partial matches, all of which are translated genomic sequences that 
   fail to match one or more motifs.

  SUMMARY INFORMATION
     24 codes involving  5 elements
      5 codes involving  4 elements
      5 codes involving  3 elements
      2 codes involving  2 elements

   COMPOSITE FINGERPRINT INDEX
  
    5|  24   24   24   24   24  
    4|   3    5    5    2    5  
    3|   2    5    5    3    0  
    2|   0    0    1    2    1  
   --+--------------------------
     |   1    2    3    4    5  

True positives..
 Q98934_CHICK   B3F205_SHEEP   RORB_RAT       RORB_MOUSE     
 B6ZGS5_HUMAN   RORB_HUMAN     Q58EY0_HUMAN   B2RDT1_HUMAN   
 RORG_HUMAN     Q6I9R9_HUMAN   B4DPR1_HUMAN   RORG_PONAB     
 B1B189_MOUSE   RORA_MOUSE     RORA_HUMAN     Q495X4_HUMAN   
 Q3U1P4_MOUSE   B6ZGS4_HUMAN   A7VL70_DANRE   B2KI74_RHIFE   
 B3KUU9_HUMAN   Q3TVH3_MOUSE   RORG_MOUSE     A3R3J9_DANRE   
Subfamily:  Codes involving 4 elements
 Subfamily True positives..
 B6ZGS6_HUMAN   A3QU33_BOVIN   Q3U513_MOUSE   B0JZJ5_DANRE   
 Q7ZU39_DANRE   
Subfamily:  Codes involving 3 elements
 Subfamily True positives..
 Q08D40_XENTR   Q3UUW3_MOUSE   B8JJ08_DANRE   A3R3K0_DANRE   
 B8JI61_DANRE   
Subfamily:  Codes involving 2 elements
 Subfamily True positives..
 B5DFL4_RAT     Q5XG07_XENLA   


  PROTEIN TITLES
   Q98934_CHICK     Nuclear orphan receptor ROR-beta - Gallus gallus 
   B3F205_SHEEP     Retinoid-related orphan receptor beta - Ovis aries 
   RORB_RAT         Nuclear receptor ROR-beta - Rattus norvegicus 
   RORB_MOUSE       Nuclear receptor ROR-beta - Mus musculus 
   B6ZGS5_HUMAN     Retinoid-related orphan receptor beta - Homo sapiens 
   RORB_HUMAN       Nuclear receptor ROR-beta - Homo sapiens 
   Q58EY0_HUMAN     RAR-related orphan receptor B - Homo sapiens 
   B2RDT1_HUMAN     cDNA, FLJ96754, highly similar to Homo sapiens RAR-related o
   RORG_HUMAN       Nuclear receptor ROR-gamma - Homo sapiens 
   Q6I9R9_HUMAN     RAR-related orphan receptor C - Homo sapiens 
   B4DPR1_HUMAN     cDNA FLJ58518, highly similar to Nuclear receptor ROR-gamma 
   RORG_PONAB       Nuclear receptor ROR-gamma - Pongo abelii 
   B1B189_MOUSE     RAR-related orphan receptor alpha - Mus musculus 
   RORA_MOUSE       Nuclear receptor ROR-alpha - Mus musculus 
   RORA_HUMAN       Nuclear receptor ROR-alpha - Homo sapiens 
   Q495X4_HUMAN     RAR-related orphan receptor A - Homo sapiens 
   Q3U1P4_MOUSE     Putative uncharacterized protein - Mus musculus 
   B6ZGS4_HUMAN     Retinoid-related orphan receptor alpha - Homo sapiens 
   A7VL70_DANRE     Retinoid-related orphan receptor alpha 2 - Danio rerio 
   B2KI74_RHIFE     RAR-related orphan receptor C isoform a (Predicted) - Rhinol
   B3KUU9_HUMAN     cDNA FLJ40675 fis, clone THYMU2021714, highly similar to NUC
   Q3TVH3_MOUSE     Putative uncharacterized protein - Mus musculus 
   RORG_MOUSE       Nuclear receptor ROR-gamma - Mus musculus 
   A3R3J9_DANRE     Retinoid-related orphan receptor b - Danio rerio 
 
   B6ZGS6_HUMAN     Retinoid-related orphan receptor gamma - Homo sapiens 
   A3QU33_BOVIN     RAR-related orphan receptor C - Bos taurus 
   Q3U513_MOUSE     Putative uncharacterized protein - Mus musculus 
   B0JZJ5_DANRE     Rorab protein - Danio rerio 
   Q7ZU39_DANRE     RAR-related orphan receptor A, paralog b - Danio rerio 
 
   Q08D40_XENTR     RAR-related orphan receptor A - Xenopus tropicalis 
   Q3UUW3_MOUSE     Putative uncharacterized protein - Mus musculus 
   B8JJ08_DANRE     Novel protein similar to vertebrate RAR-related orphan recep
   A3R3K0_DANRE     Retinoid-related orphan receptor c - Danio rerio 
   B8JI61_DANRE     RAR-related orphan receptor G - Danio rerio 
 
   B5DFL4_RAT       Rorc protein - Rattus norvegicus 
   Q5XG07_XENLA     LOC495242 protein - Xenopus laevis 

SCAN HISTORY SPTR37_10f 1 50 NSINGLE SPTR57.15_40.15f 3 300 NSINGLE INITIAL MOTIF SETS RORNUCRECPTR1 Length of motif = 22 Motif number = 1 Nuclear receptor ROR family motif I - 1 PCODE ST INT SFTNGETSPTVSMAELEHLAQN ROR3_HUMAN 283 283 SFTNGETSPTVSMAELEHLAQN ROR2_HUMAN 291 291 SFTNGETSPTVSMAELEHLAQN ROR1_MOUSE 258 258 SFTNGETSPTVSMAELEHLAQN ROR4_HUMAN 203 203 SFNNGQLAPGITMSEIDRIAQN RORB_RAT 197 197 SFCSAPEVPYASLTDIEYLVQN RORG_MOUSE 253 253 RORNUCRECPTR2 Length of motif = 14 Motif number = 2 Nuclear receptor ROR family motif II - 1 PCODE ST INT KSHLETCQYLREEL ROR3_HUMAN 307 2 KSHLETCQYLREEL ROR2_HUMAN 315 2 KSHLETCQYLREEL ROR1_MOUSE 282 2 KSHLETCQYLREEL ROR4_HUMAN 227 2 KSHLETCQYTMEEL RORB_RAT 221 2 KSFRETCQLRLEDL RORG_MOUSE 277 2 RORNUCRECPTR3 Length of motif = 18 Motif number = 3 Nuclear receptor ROR family motif III - 1 PCODE ST INT FLQEEIENYQNKQREVMW ROR3_HUMAN 328 7 FLQEEIENYQNKQREVMW ROR2_HUMAN 336 7 FLQEEIENYQNKQREVMW ROR1_MOUSE 303 7 FLQEEIENYQNKQREVMW ROR4_HUMAN 248 7 HTYEEIKAYQSKSREALW RORB_RAT 242 7 FSREEVTSYQRKSMWEMW RORG_MOUSE 298 7 RORNUCRECPTR4 Length of motif = 18 Motif number = 4 Nuclear receptor ROR family motif IV - 1 PCODE ST INT TVYFDGKYASPDVFKSLG ROR3_HUMAN 403 57 TVYFDGKYASPDVFKSLG ROR2_HUMAN 411 57 TVYFDGKYASPDVFKSLG ROR1_MOUSE 378 57 TVYFDGKYASPDVFKSLG ROR4_HUMAN 323 57 TVLFEGKYGGMQMFKALG RORB_RAT 317 57 TVFFEGKYGGVELFRALG RORG_MOUSE 373 57 RORNUCRECPTR5 Length of motif = 11 Motif number = 5 Nuclear receptor ROR family motif V - 1 PCODE ST INT PDIVRLHFPPL ROR3_HUMAN 521 4 PDIVRLHFPPL ROR2_HUMAN 529 4 PDIVRLHFPPL ROR1_MOUSE 496 4 PDIVRLHFPPL ROR4_HUMAN 441 4 PDIVNTLFPPL RORB_RAT 435 4 PIVVQAAFPPL RORG_MOUSE 489 4 FINAL MOTIF SETS RORNUCRECPTR1 Length of motif = 22 Motif number = 1 Nuclear receptor ROR family motif I - 3 PCODE ST INT SFNNGQLAPGISMTEIDRIAQN Q98934_CHICK 197 197 SFNNGQLAPGITMSEIDRIAQN B3F205_SHEEP 197 197 SFNNGQLAPGITMSEIDRIAQN RORB_RAT 208 208 SFNNGQLAPGITMSEIDRIAQN RORB_MOUSE 208 208 SFNNGQLAPGITMTEIDRIAQN B6ZGS5_HUMAN 197 197 SFNNGQLAPGITMTEIDRIAQN RORB_HUMAN 208 208 SFNNGQLAPGITMTEIDRIAQN Q58EY0_HUMAN 197 197 SFRSTPEAPYASLTEIEHLVQS B2RDT1_HUMAN 255 255 SFRSTPEAPYASLTEIEHLVQS RORG_HUMAN 255 255 SFRSTPEAPYASLTEIEHLVQS Q6I9R9_HUMAN 255 255 SFRSTPEAPYASLTEIEHLVQS B4DPR1_HUMAN 309 309 SFRSTPEAPYASLTEIEHLVQS RORG_PONAB 255 255 SFTNGETSPTVSMAELEHLAQN B1B189_MOUSE 258 258 SFTNGETSPTVSMAELEHLAQN RORA_MOUSE 258 258 SFTNGETSPTVSMAELEHLAQN RORA_HUMAN 291 291 SFTNGETSPTVSMAELEHLAQN Q495X4_HUMAN 203 203 SFTNGETSPTVSMAELEHLAQN Q3U1P4_MOUSE 202 202 SFTNGETSPTVSMAELEHLAQN B6ZGS4_HUMAN 258 258 SFTNGETSPTVSMAELEHLAQN A7VL70_DANRE 203 203 SFRSTPEAPYASLTEIEHLLQN B2KI74_RHIFE 254 254 SFRSTPEAPYASLTEIEHLVQS B3KUU9_HUMAN 234 234 SFCSAPEVPYASLTDIEYLVQN Q3TVH3_MOUSE 253 253 SFCSAPEVPYASLTDIEYLVQN RORG_MOUSE 253 253 SYQDSQLAPGVSMGELDRIAQN A3R3J9_DANRE 203 203 RORNUCRECPTR2 Length of motif = 14 Motif number = 2 Nuclear receptor ROR family motif II - 3 PCODE ST INT KSHLETCQYTMEEL Q98934_CHICK 221 2 KSHLETCQYTMEEL B3F205_SHEEP 221 2 KSHLETCQYTMEEL RORB_RAT 232 2 KSHLETCQYTMEEL RORB_MOUSE 232 2 KSHLETCQYTMEEL B6ZGS5_HUMAN 221 2 KSHLETCQYTMEEL RORB_HUMAN 232 2 KSHLETCQYTMEEL Q58EY0_HUMAN 221 2 KSYRETCQLRLEDL B2RDT1_HUMAN 279 2 KSYRETCQLRLEDL RORG_HUMAN 279 2 KSYRETCQLRLEDL Q6I9R9_HUMAN 279 2 KSYRETCQLRLEDL B4DPR1_HUMAN 333 2 KSYRETCQLRLEDL RORG_PONAB 279 2 KSHLETCQYLREEL B1B189_MOUSE 282 2 KSHLETCQYLREEL RORA_MOUSE 282 2 KSHLETCQYLREEL RORA_HUMAN 315 2 KSHLETCQYLREEL Q495X4_HUMAN 227 2 KSHLETCQYLREEL Q3U1P4_MOUSE 226 2 KSHLETCQYLREEL B6ZGS4_HUMAN 282 2 KSHMETCQYLREEL A7VL70_DANRE 227 2 KSYRETCQLRLEDL B2KI74_RHIFE 278 2 KSYRETCQLRLEDL B3KUU9_HUMAN 258 2 KSFRETCQLRLEDL Q3TVH3_MOUSE 277 2 KSFRETCQLRLEDL RORG_MOUSE 277 2 KSHLETCQYTAEEL A3R3J9_DANRE 227 2 RORNUCRECPTR3 Length of motif = 18 Motif number = 3 Nuclear receptor ROR family motif III - 3 PCODE ST INT HTYEEIKVYQSKTREALW Q98934_CHICK 242 7 HTYEEIKAYQSKSREALW B3F205_SHEEP 242 7 HTYEEIKAYQSKSREALW RORB_RAT 253 7 HTYEEIKAYQSKSREALW RORB_MOUSE 253 7 HTYEEIKAYQSKSREALW B6ZGS5_HUMAN 242 7 HTYEEIKAYQSKSREALW RORB_HUMAN 253 7 HTYEEIKAYQSKSREALW Q58EY0_HUMAN 242 7 FSREEVTGYQRKSMWEMW B2RDT1_HUMAN 300 7 FSREEVTGYQRKSMWEMW RORG_HUMAN 300 7 FSREEVTGYQRKSMWEMW Q6I9R9_HUMAN 300 7 FSREEVTGYQRKSMWEMW B4DPR1_HUMAN 354 7 FSREEVTGYQRKSMWEMW RORG_PONAB 300 7 FLQEEIENYQNKQREVMW B1B189_MOUSE 303 7 FLQEEIENYQNKQREVMW RORA_MOUSE 303 7 FLQEEIENYQNKQREVMW RORA_HUMAN 336 7 FLQEEIENYQNKQREVMW Q495X4_HUMAN 248 7 FLQEEIENYQNKQREVMW Q3U1P4_MOUSE 247 7 FLQEEIENYQNKQREVMW B6ZGS4_HUMAN 303 7 FLQEEVENYQSKPREVMW A7VL70_DANRE 248 7 FSREEVASYQRKSVWEMW B2KI74_RHIFE 299 7 FSREEVTGYQRKSMWEMW B3KUU9_HUMAN 279 7 FSREEVTSYQRKSMWEMW Q3TVH3_MOUSE 298 7 FSREEVTSYQRKSMWEMW RORG_MOUSE 298 7 HSYEEVKMYQSKTRDVLW A3R3J9_DANRE 248 7 RORNUCRECPTR4 Length of motif = 18 Motif number = 4 Nuclear receptor ROR family motif IV - 3 PCODE ST INT TVLFEGKYGGMQMFKALG Q98934_CHICK 317 57 TVLFEGKYGGMQMFKALG B3F205_SHEEP 317 57 TVLFEGKYGGMQMFKALG RORB_RAT 328 57 TVLFEGKYGGMQMFKALG RORB_MOUSE 328 57 TVLFEGKYGGMQMFKALG B6ZGS5_HUMAN 317 57 TVLFEGKYGGMQMFKALG RORB_HUMAN 328 57 TVLFEGKYGGMQMFKALG Q58EY0_HUMAN 317 57 TVFFEGKYGGMELFRALG B2RDT1_HUMAN 375 57 TVFFEGKYGGMELFRALG RORG_HUMAN 375 57 TVFFEGKYGGMELFRALG Q6I9R9_HUMAN 375 57 TVFFEGKYGGMELFRALG B4DPR1_HUMAN 429 57 TVFFEGKYGGMELFRALG RORG_PONAB 375 57 TVYFDGKYASPDVFKSLG B1B189_MOUSE 378 57 TVYFDGKYASPDVFKSLG RORA_MOUSE 378 57 TVYFDGKYASPDVFKSLG RORA_HUMAN 411 57 TVYFDGKYASPDVFKSLG Q495X4_HUMAN 323 57 TVYFDGKYASPDVFKSLG Q3U1P4_MOUSE 322 57 TVYFDGKYASPDVFKSLG B6ZGS4_HUMAN 378 57 TVYFDGKYAGPDVFKSLG A7VL70_DANRE 323 57 TVFFEGKYGGVELFRALG B2KI74_RHIFE 374 57 TVFFEGKYGGMELFRALG B3KUU9_HUMAN 354 57 TVFFEGKYGGVELFRALG Q3TVH3_MOUSE 373 57 TVFFEGKYGGVELFRALG RORG_MOUSE 373 57 TVLFEGKYGGMQIFKTLG A3R3J9_DANRE 323 57 RORNUCRECPTR5 Length of motif = 11 Motif number = 5 Nuclear receptor ROR family motif V - 3 PCODE ST INT PDIVNTLFPPL Q98934_CHICK 435 100 PDIVNTLFPPL B3F205_SHEEP 435 100 PDIVNTLFPPL RORB_RAT 446 100 PDIVNTLFPPL RORB_MOUSE 446 100 PEIVNTLFPPL B6ZGS5_HUMAN 435 100 PEIVNTLFPPL RORB_HUMAN 446 100 PEIVNTLFPPL Q58EY0_HUMAN 435 100 PIVVQAAFPPL B2RDT1_HUMAN 491 98 PIVVQAAFPPL RORG_HUMAN 491 98 PIVVQAAFPPL Q6I9R9_HUMAN 491 98 PIVVQAAFPPL B4DPR1_HUMAN 545 98 PIVVQATFPPL RORG_PONAB 491 98 PDIVRLHFPPL B1B189_MOUSE 496 100 PDIVRLHFPPL RORA_MOUSE 496 100 PDIVRLHFPPL RORA_HUMAN 529 100 PDIVRLHFPPL Q495X4_HUMAN 441 100 PDIVRLHFPPL Q3U1P4_MOUSE 440 100 PDIVRLHFPPL B6ZGS4_HUMAN 496 100 PDIVRAHFPPL A7VL70_DANRE 441 100 PIVVQAAFPPL B2KI74_RHIFE 490 98 PIVAQAAFPPL B3KUU9_HUMAN 470 98 PIVVQAAFPPL Q3TVH3_MOUSE 489 98 PIVVQAAFPPL RORG_MOUSE 489 98 PETVNMLFPPL A3R3J9_DANRE 441 100

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