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PR00350

Identifier
VITAMINDR  [View Relations]  [View Alignment]  
Accession
PR00350
No. of Motifs
6
Creation Date
11-MAY-1995  (UPDATE 23-JUN-1999)
Title
Vitamin D receptor (1I nuclear receptor) signature
Database References
PRINTS; PR00398 STRDHORMONER
INTERPRO; IPR000324
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).

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].
 
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
   7 codes involving  6 elements
0 codes involving 5 elements
2 codes involving 4 elements
1 codes involving 3 elements
13 codes involving 2 elements
Composite Feature Index
6777777
5000000
4222020
3100011
2961451
123456
True Positives
VDR_BOVIN     VDR_CHICK     VDR_COTJA     VDR_HUMAN     
VDR_MOUSE VDR_RAT VDR_XENLA
True Positive Partials
Codes involving 4 elements
PXR_HUMAN PXR_MOUSE
Codes involving 3 elements
Q14994
Codes involving 2 elements
ECR_BOMMO ECR_CHITE ECR_DROME ECR_HELVI
ECR_LUCCU ECR_MANSE NER_HUMAN O35627
Q60644 Q62694 Q62755 Q91839
Q92943
Sequence Titles
VDR_BOVIN   VITAMIN D3 RECEPTOR (VDR) (1,25-DIHYDROXYVITAMIN D3 RECEPTOR) - BOS TAURUS (BOVINE). 
VDR_CHICK VITAMIN D3 RECEPTOR (VDR) (1,25-DIHYDROXYVITAMIN D3 RECEPTOR) - GALLUS GALLUS (CHICKEN).
VDR_COTJA VITAMIN D3 RECEPTOR (VDR) (1,25-DIHYDROXYVITAMIN D3 RECEPTOR) - COTURNIX COTURNIX JAPONICA (JAPANESE QUAIL).
VDR_HUMAN VITAMIN D3 RECEPTOR (VDR) (1,25-DIHYDROXYVITAMIN D3 RECEPTOR) - HOMO SAPIENS (HUMAN).
VDR_MOUSE VITAMIN D3 RECEPTOR (VDR) (1,25-DIHYDROXYVITAMIN D3 RECEPTOR) - MUS MUSCULUS (MOUSE).
VDR_RAT VITAMIN D3 RECEPTOR (VDR) (1,25-DIHYDROXYVITAMIN D3 RECEPTOR) - RATTUS NORVEGICUS (RAT).
VDR_XENLA VITAMIN D3 RECEPTOR (VDR) (1,25-DIHYDROXYVITAMIN D3 RECEPTOR) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).

PXR_HUMAN ORPHAN NUCLEAR RECEPTOR PXR (PREGNANE X RECEPTOR) - HOMO SAPIENS (HUMAN).
PXR_MOUSE ORPHAN NUCLEAR RECEPTOR PXR (PREGNANE X RECEPTOR) - MUS MUSCULUS (MOUSE).

Q14994 ORPHAN NUCLEAR HORMONE RECEPTOR - HOMO SAPIENS (HUMAN).

ECR_BOMMO ECDYSONE RECEPTOR (ECDYSTEROID RECEPTOR) (20-HYDROXY-ECDYSONE RECEPTOR) (20E REC
ECR_CHITE ECDYSONE RECEPTOR (ECDYSTEROID RECEPTOR) (20-HYDROXY-ECDYSONE RECEPTOR) (20E REC
ECR_DROME ECDYSONE RECEPTOR (ECDYSTEROID RECEPTOR) (20-HYDROXY-ECDYSONE RECEPTOR) (20E REC
ECR_HELVI ECDYSONE RECEPTOR (ECDYSTEROID RECEPTOR) (20-HYDROXY-ECDYSONE RECEPTOR) (20E REC
ECR_LUCCU ECDYSONE RECEPTOR (ECDYSTEROID RECEPTOR) (20-HYDROXY-ECDYSONE RECEPTOR) (20E REC
ECR_MANSE ECDYSONE RECEPTOR (ECDYSTEROID RECEPTOR) (20-HYDROXY-ECDYSONE RECEPTOR) (20E REC
NER_HUMAN NUCLEAR RECEPTOR NER (UBIQUITOUSLY-EXPRESSED NUCLEAR RECEPTOR) - HOMO SAPIENS (HUMAN).
O35627 MCAR1 - MUS MUSCULUS (MOUSE).
Q60644 UBIQUITOUSLY-EXPRESSED NUCLEAR RECEPTOR (RETINOID X RECEPTOR INTERACTING PROTEIN NO.15) - MUS MUSCULUS (MOUSE).
Q62694 ORPHAN RECEPTOR - RATTUS NORVEGICUS (RAT).
Q62755 ORPHAN NUCLEAR RECEPTOR OR-1 - RATTUS NORVEGICUS (RAT).
Q91839 ORPHAN NUCLEAR RECEPTOR OF STEROID/THYROID SUPERFAMILY - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
Q92943 FARNESOL RECEPTOR HRR-1 - HOMO SAPIENS (HUMAN).
Scan History
OWL26_0    2  100  NSINGLE    
SPTR37_9f 2 20 NSINGLE
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
CGVCGDRATGFHFNAMT VDR_HUMAN 24 24 -
CGVCGDRATGFHFNAMT VDR_RAT 24 24 -

Motif 2 width=20
Element Seqn Id St Int Rpt
CEGCKGFFRRSMKRKALFTC VDR_HUMAN 41 0 -
CEGCKGFFRRSMKRKALFTC VDR_RAT 41 0 -

Motif 3 width=22
Element Seqn Id St Int Rpt
EEQQRIIAILLDAHHKTYDPTY VDR_HUMAN 126 65 -
EEQQHIIAILLDAHHKTYDPTY VDR_RAT 126 65 -

Motif 4 width=21
Element Seqn Id St Int Rpt
DYKYRVSDVTKAGHSLELIEP VDR_HUMAN 292 144 -
DYKYDVTDVSKAGHTLELIEP VDR_RAT 288 140 -

Motif 5 width=20
Element Seqn Id St Int Rpt
VLLMAICIVSPDRPGVQDAA VDR_HUMAN 331 18 -
VLLMAICIVSPDRPGVQDAK VDR_RAT 327 18 -

Motif 6 width=24
Element Seqn Id St Int Rpt
LYAKMIQKLADLRSLNEEHSKQYR VDR_HUMAN 379 28 -
LYAKMIQKLADLRSLNEEHSKQYR VDR_RAT 375 28 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
CGVCGDRATGFHFNAMT VDR_HUMAN 24 24 -
CGVCGDRATGFHFNAMT VDR_BOVIN 21 21 -
CGVCGDRATGFHFNAMT VDR_RAT 24 24 -
CGVCGDRATGFHFNAMT VDR_MOUSE 24 24 -
CGVCGDRATGFHFNAMT VDR_COTJA 44 44 -
CGVCGDRATGFHFNAMT VDR_CHICK 47 47 -
CGVCGDKATGFHFNAMT VDR_XENLA 25 25 -

Motif 2 width=20
Element Seqn Id St Int Rpt
CEGCKGFFRRSMKRKALFTC VDR_HUMAN 41 0 -
CEGCKGFFRRSMKRKALFTC VDR_BOVIN 38 0 -
CEGCKGFFRRSMKRKALFTC VDR_RAT 41 0 -
CEGCKGFFRRSMKRKALFTC VDR_MOUSE 41 0 -
CEGCKGFFRRSMKRKAMFTC VDR_COTJA 61 0 -
CEGCKGFFRRSMKRKAMFTC VDR_CHICK 64 0 -
CEGCKGFFRRSMKRKAMFTC VDR_XENLA 42 0 -

Motif 3 width=22
Element Seqn Id St Int Rpt
EEQQRIIAILLDAHHKTYDPTY VDR_HUMAN 126 65 -
EEQQRIIAILLDAHHKTYDPTY VDR_BOVIN 123 65 -
EEQQHIIAILLDAHHKTYDPTY VDR_RAT 126 65 -
EEQQHIIAILLDAHHKTYDPTY VDR_MOUSE 126 65 -
EEQQKVINILLEAHHKTFDTTY VDR_COTJA 146 65 -
EEQQKVIDTLLEAHHKTFDTTY VDR_CHICK 149 65 -
DEQQKMIDILLEAHRKTFDTTY VDR_XENLA 127 65 -

Motif 4 width=21
Element Seqn Id St Int Rpt
DYKYRVSDVTKAGHSLELIEP VDR_HUMAN 292 144 -
DYKYRVSDVTKAGHSLELIEP VDR_BOVIN 289 144 -
DYKYDVTDVSKAGHTLELIEP VDR_RAT 288 140 -
DYKYDITDVSRAGHTLELIEP VDR_MOUSE 287 139 -
DFKYKVSDVTQAGHSMDLLEP VDR_COTJA 313 145 -
DFKYKVSDVTQAGHSMDLLEP VDR_CHICK 316 145 -
DFKYKVDDVTQAGHNMELLEP VDR_XENLA 287 138 -

Motif 5 width=20
Element Seqn Id St Int Rpt
VLLMAICIVSPDRPGVQDAA VDR_HUMAN 331 18 -
VLLMAICIVSPDRPGVQDAA VDR_BOVIN 328 18 -
VLLMAICIVSPDRPGVQDAK VDR_RAT 327 18 -
VLLMAICIVSPDRPGVQDAK VDR_MOUSE 326 18 -
VLLMAICILSPDRPGVQDTS VDR_COTJA 352 18 -
VLLMAICILSPDRPGVQDTS VDR_CHICK 355 18 -
VLLMAICILSPDRPGLQDKA VDR_XENLA 326 18 -

Motif 6 width=24
Element Seqn Id St Int Rpt
LYAKMIQKLADLRSLNEEHSKQYR VDR_HUMAN 379 28 -
LYAKMIQKLADLRSLNEEHSKQYR VDR_BOVIN 376 28 -
LYAKMIQKLADLRSLNEEHSKQYR VDR_RAT 375 28 -
LYAKMIQKLADLRSLNEEHSKQYR VDR_MOUSE 374 28 -
LYAKMIQKLADLRSLNEEHSKQYR VDR_COTJA 400 28 -
LYAKMIQKLADLRSLNEEHSKQYR VDR_CHICK 403 28 -
LYAKMIQKLADLRSLNEEHSKQYR VDR_XENLA 374 28 -