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"