WORKLIST ENTRIES (1):

VITAMINDR View alignment View Structure       Vitamin D receptor signature
 Type of fingerprint: COMPOUND with 6  elements
Links:
   PRINTS; PR00047 STROIDFINGER; PR00398 STRDHORMONER
   PRINTS; PR00521 ANDROGENR; PR01282 COUPTNFACTOR; PR01283 ECDYSTEROIDR
   PRINTS; PR00528 GLCORTICOIDR; PR01284 NUCLEARECPTR; PR00543 OESTROGENR
   PRINTS; PR00544 PROGESTRONER; PR01288 PROXISOMEPAR; PR00545 RETINOIDXR
   PRINTS; PR01293 RORNUCRECPTR; PR00546 THYROIDHORMR; PR02034 LIVERXRECPTR
   INTERPRO; IPR000324
   PDB; 1KB2 3Dinfo; 1KB6 3Dinfo; 1IE8 3Dinfo; 1S0Z 3Dinfo; 2HAM 3Dinfo; 3M7R 3Dinfo
   SCOP; 1KB2; 1KB6; 1IE8; 1S0Z; 2HAM
   CATH; 1KB2; 1KB6; 1IE8; 1S0Z; 2HAM
   MIM; 601769

 Creation date 06-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).

   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].
  
   The vitamin D receptor (VDR) mediates the signal of 1-a,25-dihydroxyvitamin 
   D3 by binding to vitamin D responsive elements - it functions either as a 
   homodimer, or as a heterodimer of vitamin D and retinoid X receptor
   subunits. Deficiency of VDR causes type IIA rickets [2].  
  
   VITAMINDR is a 6-element fingerprint that provides a signature for the
   vitamin D receptors. The fingerprint was derived from an initial alignment
   of 7 sequences: motif 1 encodes part of the zinc finger region; motif 2 
   resides wholly within the zinc finger region; motifs 3 and 4 lie in the
   hinge region; and motifs 5 and 6 reside in the ligand-binding domain.
   Three iterations on SPTR57.15_40.15f were required to reach convergence, at 
   which point a true set comprising 24 sequences was identified. Four partial 
   matches were also found, all of which are translated nucleotide sequences 
   that fail to match one or more motifs.

  SUMMARY INFORMATION
     24 codes involving  6 elements
      2 codes involving  5 elements
      1 codes involving  4 elements
      1 codes involving  3 elements
      0 codes involving  2 elements

   COMPOSITE FINGERPRINT INDEX
  
    6|  24   24   24   24   24   24  
    5|   1    2    2    2    2    1  
    4|   0    1    1    0    1    1  
    3|   1    1    1    0    0    0  
    2|   0    0    0    0    0    0  
   --+-------------------------------
     |   1    2    3    4    5    6  

True positives..
 VDR_BOVIN      B2CCA0_ORYLA   VDR_SAGOE      Q14RR3_SALSA   
 Q6H8I7_SALSA   B2CCA1_ORYLA   Q9IB73_PAROL   Q5R8V3_PONAB   
 VDRA_DANRE     Q9IB74_PAROL   Q5DVI8_CYPCA   B6ZGT0_HUMAN   
 VDR_HUMAN      VDR_RAT        VDRB_DANRE     VDR_PIG        
 VDR_CHICK      Q3U0J7_MOUSE   VDR_MOUSE      Q922X0_MOUSE   
 Q4FJV8_MOUSE   B7ZPA5_XENLA   VDR_XENLA      VDR_COTJA      
Subfamily:  Codes involving 5 elements
 Subfamily True positives..
 Q14RR2_SALSA   B4DRV7_HUMAN   
Subfamily:  Codes involving 4 elements
 Subfamily True positives..
 Q7ZZY9_PETMA   
Subfamily:  Codes involving 3 elements
 Subfamily True positives..
 Q4SSA9_TETNG   


  PROTEIN TITLES
   VDR_BOVIN        Vitamin D3 receptor - Bos taurus 
   B2CCA0_ORYLA     Vitamin D receptor alpha - Oryzias latipes 
   VDR_SAGOE        Vitamin D3 receptor - Saguinus oedipus 
   Q14RR3_SALSA     Hypothetical vitamin D receptor - Salmo salar 
   Q6H8I7_SALSA     Vitamin D receptor - Salmo salar 
   B2CCA1_ORYLA     Vitamin D receptor beta - Oryzias latipes 
   Q9IB73_PAROL     Vitamin D receptor a - Paralichthys olivaceus 
   Q5R8V3_PONAB     Putative uncharacterized protein DKFZp469H1213 - Pongo abeli
   VDRA_DANRE       Vitamin D3 receptor A - Danio rerio 
   Q9IB74_PAROL     Vitamin D receptor b - Paralichthys olivaceus 
   Q5DVI8_CYPCA     Vitamin D receptor I - Cyprinus carpio 
   B6ZGT0_HUMAN     Vitamin D (1,25-dihydroxyvitamin D3) receptor - Homo sapiens
   VDR_HUMAN        Vitamin D3 receptor - Homo sapiens 
   VDR_RAT          Vitamin D3 receptor - Rattus norvegicus 
   VDRB_DANRE       Vitamin D3 receptor B - Danio rerio 
   VDR_PIG          Vitamin D3 receptor - Sus scrofa 
   VDR_CHICK        Vitamin D3 receptor - Gallus gallus 
   Q3U0J7_MOUSE     Putative uncharacterized protein - Mus musculus 
   VDR_MOUSE        Vitamin D3 receptor - Mus musculus 
   Q922X0_MOUSE     Putative uncharacterized protein - Mus musculus 
   Q4FJV8_MOUSE     Vdr protein - Mus musculus 
   B7ZPA5_XENLA     Vitamin D (1,25-dihydroxyvitamin D3) receptor - Xenopus laev
   VDR_XENLA        Vitamin D3 receptor - Xenopus laevis 
   VDR_COTJA        Vitamin D3 receptor - Coturnix coturnix japonica 
 
   Q14RR2_SALSA     Hypothetical vitamin D receptor - Salmo salar 
   B4DRV7_HUMAN     cDNA FLJ51539, highly similar to Vitamin D3 receptor - Homo 
 
   Q7ZZY9_PETMA     Vitamin D receptor - Petromyzon marinus 
 
   Q4SSA9_TETNG     Chromosome undetermined SCAF14476, whole genome shotgun sequ

SCAN HISTORY SPTR57.15_40.15f 3 300 NSINGLE INITIAL MOTIF SETS VITAMINDR1 Length of motif = 12 Motif number = 1 Vitamin D receptor motif I - 1 PCODE ST INT GDFDRNVPRICG VDR_PIG 14 14 GDFDRNVPRICG VDR_CHICK 37 37 MEFDKNVPRICG VDR_XENLA 15 15 DEFDRNAPRICG Q9IB73_PAROL 14 14 DEFDRNVPRICG B2CCA1_ORYLA 14 14 GDFDRNVPRICG VDR_HUMAN 14 14 DEFDRNAPRICG Q14RR3_SALSA 14 14 VITAMINDR2 Length of motif = 12 Motif number = 2 Vitamin D receptor motif II - 1 PCODE ST INT FNGDCRITKDNR VDR_PIG 62 36 FNGDCKITKDNR VDR_CHICK 85 36 FNGDCRITKDNR VDR_XENLA 63 36 FNGSCTITKDNR Q9IB73_PAROL 62 36 FNGSCTITKDNR B2CCA1_ORYLA 62 36 FNGDCRITKDNR VDR_HUMAN 62 36 FNGSCTITKDNR Q14RR3_SALSA 62 36 VITAMINDR3 Length of motif = 13 Motif number = 3 Vitamin D receptor motif III - 1 PCODE ST INT TYADFGQFRPPVR VDR_PIG 146 72 TYSDFNKFRPPVR VDR_CHICK 169 72 TYSDFNKFRPPVR VDR_XENLA 147 72 SYSDFSRFRPPVR Q9IB73_PAROL 146 72 SYSDFCRFRPPVR B2CCA1_ORYLA 150 76 TYSDFCQFRPPVR VDR_HUMAN 146 72 SYSDFSRFRPPVR Q14RR3_SALSA 146 72 VITAMINDR4 Length of motif = 13 Motif number = 4 Vitamin D receptor motif IV - 1 PCODE ST INT SDQYTSSPDTMEP VDR_PIG 187 28 SDAFAAFPEPMEP VDR_CHICK 211 29 SDVFTSSPDSSEH VDR_XENLA 184 24 SDSFNHSPESVDT Q9IB73_PAROL 180 21 SDSFSHSPESVDT B2CCA1_ORYLA 184 21 SDHCITSSDMMDS VDR_HUMAN 187 28 SDSFNHSPESVDT Q14RR3_SALSA 180 21 VITAMINDR5 Length of motif = 11 Motif number = 5 Vitamin D receptor motif V - 1 PCODE ST INT LVSYSIQKVIG VDR_PIG 233 33 LVSYSIQKVIG VDR_CHICK 257 33 LVSYSIQKIIG VDR_XENLA 228 31 LVSYSIQKVIG Q9IB73_PAROL 228 35 LVSYSIQKVIG B2CCA1_ORYLA 233 36 LVSYSIQKVIG VDR_HUMAN 233 33 LVSYSIQKVIG Q14RR3_SALSA 230 37 VITAMINDR6 Length of motif = 13 Motif number = 6 Vitamin D receptor motif VI - 1 PCODE ST INT GSRDYKYQVSDVA VDR_PIG 289 45 GSNDFKYKVSDVT VDR_CHICK 313 45 GSEDFKYKVDDVT VDR_XENLA 284 45 GGPDFKYCINDVT Q9IB73_PAROL 284 45 GAPDFKYQISDVT B2CCA1_ORYLA 289 45 GNQDYKYRVSDVT VDR_HUMAN 289 45 GGPDFKYCVNDVT Q14RR3_SALSA 287 46 FINAL MOTIF SETS VITAMINDR1 Length of motif = 12 Motif number = 1 Vitamin D receptor motif I - 3 PCODE ST INT GDFDRNVPRICG VDR_BOVIN 14 14 DEFDRNVPRICG B2CCA0_ORYLA 14 14 GDFDRNVPRICG VDR_SAGOE 14 14 DEFDRNAPRICG Q14RR3_SALSA 14 14 DEFDRNAPRICG Q6H8I7_SALSA 11 11 DEFDRNVPRICG B2CCA1_ORYLA 14 14 DEFDRNAPRICG Q9IB73_PAROL 14 14 GDFDRNVPRICG Q5R8V3_PONAB 14 14 DEFDRNAPRICG VDRA_DANRE 46 46 DEFDRNMPRICG Q9IB74_PAROL 14 14 DKFDRNAPRICG Q5DVI8_CYPCA 25 25 GDFDRNVPRICG B6ZGT0_HUMAN 14 14 GDFDRNVPRICG VDR_HUMAN 14 14 GDFDRNVPRICG VDR_RAT 14 14 DEFDRNVPRICG VDRB_DANRE 13 13 GDFDRNVPRICG VDR_PIG 14 14 GDFDRNVPRICG VDR_CHICK 37 37 GDFDRNVPRICG Q3U0J7_MOUSE 14 14 GDFDRNVPRICG VDR_MOUSE 14 14 GDFDRNVPRICG Q922X0_MOUSE 14 14 GDFDRNVPRICG Q4FJV8_MOUSE 14 14 MEFDKNVPRICG B7ZPA5_XENLA 15 15 MEFDKNVPRICG VDR_XENLA 15 15 PEFDRNVPRICG VDR_COTJA 34 34 VITAMINDR2 Length of motif = 12 Motif number = 2 Vitamin D receptor motif II - 3 PCODE ST INT FNGDCRITKDNR VDR_BOVIN 62 36 FNGSCNITKDNR B2CCA0_ORYLA 62 36 FNGDCRITKDNR VDR_SAGOE 62 36 FNGSCTITKDNR Q14RR3_SALSA 62 36 FNGSCTITKDNR Q6H8I7_SALSA 59 36 FNGSCTITKDNR B2CCA1_ORYLA 62 36 FNGSCTITKDNR Q9IB73_PAROL 62 36 FNGDCRITKDNR Q5R8V3_PONAB 62 36 FNGNCTITKDNR VDRA_DANRE 94 36 FNGSCTITKDNR Q9IB74_PAROL 62 36 FNGNCTITKDNR Q5DVI8_CYPCA 73 36 FNGDCRITKDNR B6ZGT0_HUMAN 62 36 FNGDCRITKDNR VDR_HUMAN 62 36 FNGDCRITKDNR VDR_RAT 62 36 FNGSCTITKDNR VDRB_DANRE 61 36 FNGDCRITKDNR VDR_PIG 62 36 FNGDCKITKDNR VDR_CHICK 85 36 FNGDCRITKDNR Q3U0J7_MOUSE 62 36 FNGDCRITKDNR VDR_MOUSE 62 36 FNGDCRITKDNR Q922X0_MOUSE 62 36 FNGDCRITKDNR Q4FJV8_MOUSE 62 36 FNGDCRITKDNR B7ZPA5_XENLA 63 36 FNGDCRITKDNR VDR_XENLA 63 36 FSGDCKITKDNR VDR_COTJA 82 36 VITAMINDR3 Length of motif = 13 Motif number = 3 Vitamin D receptor motif III - 3 PCODE ST INT TYSDFSQFRPPVR VDR_BOVIN 146 72 SYSDFSRFRPPVR B2CCA0_ORYLA 146 72 TYSDFCQFRPPVR VDR_SAGOE 146 72 SYSDFSRFRPPVR Q14RR3_SALSA 146 72 SYSDFSRFRPPVR Q6H8I7_SALSA 143 72 SYSDFCRFRPPVR B2CCA1_ORYLA 150 76 SYSDFSRFRPPVR Q9IB73_PAROL 146 72 TYSDFCQFRPPVR Q5R8V3_PONAB 146 72 SYSDFVRFRPPVR VDRA_DANRE 178 72 SYSDFCRFRPPVR Q9IB74_PAROL 150 76 SYSDFVRFRPPVR Q5DVI8_CYPCA 157 72 TYSDFCQFRPPVR B6ZGT0_HUMAN 146 72 TYSDFCQFRPPVR VDR_HUMAN 146 72 TYADFRDFRPPVR VDR_RAT 146 72 SYSDFSRFRPPVR VDRB_DANRE 145 72 TYADFGQFRPPVR VDR_PIG 146 72 TYSDFNKFRPPVR VDR_CHICK 169 72 TYADFRDFRPPIR Q3U0J7_MOUSE 146 72 TYADFRDFRPPIR VDR_MOUSE 146 72 TYADFRDFRPPIR Q922X0_MOUSE 146 72 TYADFRDFRPPIR Q4FJV8_MOUSE 146 72 TYSDFNKFRPPVR B7ZPA5_XENLA 147 72 TYSDFNKFRPPVR VDR_XENLA 147 72 TYSDFNKFRPPVR VDR_COTJA 166 72 VITAMINDR4 Length of motif = 13 Motif number = 4 Vitamin D receptor motif IV - 3 PCODE ST INT SDHCTSSPDTMEP VDR_BOVIN 185 26 SDSFNHSPESVDT B2CCA0_ORYLA 180 21 SDHYITSPDMMDS VDR_SAGOE 187 28 SDSFNHSPESVDT Q14RR3_SALSA 180 21 SDSFNHSPESVDT Q6H8I7_SALSA 177 21 SDSFSHSPESVDT B2CCA1_ORYLA 184 21 SDSFNHSPESVDT Q9IB73_PAROL 180 21 SDNCITSPDMMDS Q5R8V3_PONAB 187 28 SDSFNHSPESVDT VDRA_DANRE 212 21 SDSFSHSPESVDT Q9IB74_PAROL 184 21 SDSFNHSPESVDT Q5DVI8_CYPCA 191 21 SDHCITSSDMMDS B6ZGT0_HUMAN 187 28 SDHCITSSDMMDS VDR_HUMAN 187 28 SDLYTTSLDMMEP VDR_RAT 183 24 SDSFSHSPESGDR VDRB_DANRE 179 21 SDQYTSSPDTMEP VDR_PIG 187 28 SDAFAAFPEPMEP VDR_CHICK 211 29 SDLYTPSLDMMEP Q3U0J7_MOUSE 182 23 SDLYTPSLDMMEP VDR_MOUSE 182 23 SDLYTPSLDMMEP Q922X0_MOUSE 182 23 SDLYTPSLDMMEP Q4FJV8_MOUSE 182 23 SDVFTSSPDSSEH B7ZPA5_XENLA 184 24 SDVFTSSPDSSEH VDR_XENLA 184 24 SDAFGAFPEPMEP VDR_COTJA 208 29 VITAMINDR5 Length of motif = 11 Motif number = 5 Vitamin D receptor motif V - 3 PCODE ST INT LVSYSIQKVIG VDR_BOVIN 231 33 LVSYSIQKVIG B2CCA0_ORYLA 228 35 LVSYSIQKVIG VDR_SAGOE 233 33 LVSYSIQKVIG Q14RR3_SALSA 230 37 LVSYSIQKVIG Q6H8I7_SALSA 227 37 LVSYSIQKVIG B2CCA1_ORYLA 233 36 LVSYSIQKVIG Q9IB73_PAROL 228 35 LVSYSIQKVIG Q5R8V3_PONAB 233 33 LVSYSIQKVIG VDRA_DANRE 261 36 LVSYSIQKVIG Q9IB74_PAROL 233 36 LVSYSIQKVIG Q5DVI8_CYPCA 240 36 LVSYSIQKVIG B6ZGT0_HUMAN 233 33 LVSYSIQKVIG VDR_HUMAN 233 33 LVSYSIQKVIG VDR_RAT 229 33 LVSYSIQKVIG VDRB_DANRE 230 38 LVSYSIQKVIG VDR_PIG 233 33 LVSYSIQKVIG VDR_CHICK 257 33 LVSYSIQKVIG Q3U0J7_MOUSE 228 33 LVSYSIQKVIG VDR_MOUSE 228 33 LVSYSIQKVIG Q922X0_MOUSE 228 33 LVSYSIQKVIG Q4FJV8_MOUSE 228 33 LVSYSIQKIIG B7ZPA5_XENLA 228 31 LVSYSIQKIIG VDR_XENLA 228 31 LVSYSIQKVIG VDR_COTJA 254 33 VITAMINDR6 Length of motif = 13 Motif number = 6 Vitamin D receptor motif VI - 3 PCODE ST INT GSPDYKYQVSDVT VDR_BOVIN 288 46 GGPDFKYCVNDVT B2CCA0_ORYLA 284 45 GNPDYKYRISDVT VDR_SAGOE 289 45 GGPDFKYCVNDVT Q14RR3_SALSA 287 46 GGPDFKYCVNDVT Q6H8I7_SALSA 284 46 GAPDFKYQISDVT B2CCA1_ORYLA 289 45 GGPDFKYCINDVT Q9IB73_PAROL 284 45 GNQDYKYRISDVT Q5R8V3_PONAB 289 45 GGPDFKYCINDVT VDRA_DANRE 317 45 GAPDFKYQISDVT Q9IB74_PAROL 289 45 GGPDFKYCVNDVT Q5DVI8_CYPCA 296 45 GNQDYKYRVSDVT B6ZGT0_HUMAN 289 45 GNQDYKYRVSDVT VDR_HUMAN 289 45 GSQDYKYDVTDVS VDR_RAT 285 45 GGPEFKYCVNDVT VDRB_DANRE 286 45 GSRDYKYQVSDVA VDR_PIG 289 45 GSNDFKYKVSDVT VDR_CHICK 313 45 GSQDYKYDITDVS Q3U0J7_MOUSE 284 45 GSQDYKYDITDVS VDR_MOUSE 284 45 GSQDYKYDITDVS Q922X0_MOUSE 284 45 GSQDYKYDITDVS Q4FJV8_MOUSE 284 45 GSEDFKYKVDDVT B7ZPA5_XENLA 284 45 GSEDFKYKVDDVT VDR_XENLA 284 45 GSNDFKYKVSDVT VDR_COTJA 310 45

User query: Display/Full Code "VITAMINDR"