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PR01285

Identifier
HMRNUCRECPTR  [View Relations]  [View Alignment]  
Accession
PR01285
No. of Motifs
9
Creation Date
16-FEB-2000
Title
Orphan nuclear receptor HMR signature
Database References
PRINTS; PR00398 STRDHORMONER; PR01284 NUCLEARECPTR
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. WILSON, T.E., PAULSEN, R.E., PADGETT, K.A. AND MILBRANDT, J.
Participation of non-zinc finger residues in DNA binding by two nuclear 
orphan receptors.
SCIENCE 256 107-110 (1992). 

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].
 
NGFI-B is an early response protein and orphan member of the steroid
hormone receptor superfamily [4]. It is expressed in the lung, brain and
superior cervical ganglia, and high levels are also seen in adrenal
tissue. While members of this superfamily typically bind DNA as dimers, 
NGFI-B binds as a monomer. A domain separate from the NGFI-B zinc fingers
(the so-called A box) has been identified and is required for recognition
of two adenine-thymidine base pairs at the 5' end of the NGFI-B DNA binding
element [4].
 
HMRNUCRECPTR is a 9-element fingerprint that provides a signature for the
HMR orphan nuclear receptors. The fingerprint was derived from an initial
alignment of 4 sequences: the motifs were drawn from conserved regions
spanning virtually the full alignment length, focusing on those sections
that characterise the HMR nuclear receptors but distinguish them from the
rest of the nuclear receptor family - motifs 1-7 lie N-terminal to the
zinc finger domain; motif 8 falls after the zinc finger domain; and motif 9
resides at the C-terminus. A single iteration on SPTR37_10f was required to 
reach convergence, no further sequences being identified beyond the starting
set. A single partial match was found, Q15627, a human TR3beta fragment that
matches the N-terminal motifs. 
Summary Information
   4 codes involving  9 elements
0 codes involving 8 elements
1 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
9444444444
8000000000
7111111100
6000000000
5000000000
4000000000
3000000000
2000000000
123456789
True Positives
NR41_CANFA    NR41_HUMAN    NR41_MOUSE    NR41_RAT      
True Positive Partials
Codes involving 7 elements
Q15627
Sequence Titles
NR41_CANFA  ORPHAN NUCLEAR RECEPTOR HMR (ORPHAN NUCLEAR RECEPTOR NGFI-B) - CANIS FAMILIARIS  
NR41_HUMAN ORPHAN NUCLEAR RECEPTOR HMR (EARLY RESPONSE PROTEIN NAK1) (TR3 ORPHAN RECEPTOR)
NR41_MOUSE ORPHAN NUCLEAR RECEPTOR HMR (NUCLEAR HORMONE RECEPTOR NUR/77) (N10 NUCLEAR PROTE
NR41_RAT ORPHAN NUCLEAR RECEPTOR HMR (NERVE GROWTH FACTOR INDUCED PROTEIN I-B) (NGFI-B) (

Q15627 TR3BETA - HOMO SAPIENS (HUMAN).
Scan History
SPTR37_10f 1  25   NSINGLE    
Initial Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
TPATSPGPRDHLTGDP NR41_RAT 10 10 -
TPAPSPGPRDHLASDP NR41_HUMAN 10 10 -
TPATSPGPRDHLTGDP NR41_MOUSE 10 10 -
TPAPSPGPRDHLASDP NR41_CANFA 10 10 -

Motif 2 width=13
Element Seqn Id St Int Rpt
SPETAPTAPATLP NR41_RAT 39 13 -
SPEAAPAAPTALP NR41_HUMAN 39 13 -
SPETAPAAPATLP NR41_MOUSE 39 13 -
SPEAAPTAPTALP NR41_CANFA 39 13 -

Motif 3 width=13
Element Seqn Id St Int Rpt
LPGTAQPCSSASS NR41_RAT 72 20 -
LPGTVQPCSSASS NR41_HUMAN 71 19 -
LPGTTQPCSSACS NR41_MOUSE 71 19 -
LPGTAQPCSSASS NR41_CANFA 71 19 -

Motif 4 width=12
Element Seqn Id St Int Rpt
ATSPASASFKFE NR41_RAT 92 7 -
ATSPASASFKFE NR41_HUMAN 93 9 -
ATSPASASFKFE NR41_MOUSE 95 11 -
ATSPASASFKFE NR41_CANFA 93 9 -

Motif 5 width=20
Element Seqn Id St Int Rpt
PPTFFSFSPPTGPSPSLAQS NR41_RAT 185 81 -
PPAFFSFSPPTGPSPSLAQS NR41_HUMAN 186 81 -
PPTFFSFSPPTGPSPSLAQS NR41_MOUSE 189 82 -
PPAFFSFSPPTGPSPSLAQS NR41_CANFA 186 81 -

Motif 6 width=17
Element Seqn Id St Int Rpt
ATHQLGEGESYSVPAAF NR41_RAT 213 8 -
ATHQLGEGESYSMPTAF NR41_HUMAN 214 8 -
ATHQLGEGESYSMPAAF NR41_MOUSE 217 8 -
ATCQLGERESYSISTAF NR41_CANFA 214 8 -

Motif 7 width=16
Element Seqn Id St Int Rpt
GLAPTSPNCDTSGILD NR41_RAT 231 1 -
GLAPTSPHLEGSGILD NR41_HUMAN 232 1 -
GLAPTSPNRDTSGILD NR41_MOUSE 235 1 -
GLAPTSPHLDGPGMLD NR41_CANFA 232 1 -

Motif 8 width=15
Element Seqn Id St Int Rpt
KQPPDASPTNLLTSL NR41_RAT 353 106 -
KQPPDASPANLLTSL NR41_HUMAN 354 106 -
KQPPDASPTNLLTSL NR41_MOUSE 357 106 -
KQPPDASPANLLTSL NR41_CANFA 354 106 -

Motif 9 width=16
Element Seqn Id St Int Rpt
EHMAAVAGDPQPASCL NR41_RAT 536 168 -
EHVAAVAGEPQPASCL NR41_HUMAN 537 168 -
EHMATVAGDPQPASCL NR41_MOUSE 540 168 -
EHVSAVAGEPQPASCL NR41_CANFA 537 168 -
Final Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
TPATSPGPRDHLTGDP NR41_RAT 10 10 -
TPAPSPGPRDHLASDP NR41_HUMAN 10 10 -
TPATSPGPRDHLTGDP NR41_MOUSE 10 10 -
TPAPSPGPRDHLASDP NR41_CANFA 10 10 -

Motif 2 width=13
Element Seqn Id St Int Rpt
SPETAPTAPATLP NR41_RAT 39 13 -
SPEAAPAAPTALP NR41_HUMAN 39 13 -
SPETAPAAPATLP NR41_MOUSE 39 13 -
SPEAAPTAPTALP NR41_CANFA 39 13 -

Motif 3 width=13
Element Seqn Id St Int Rpt
LPGTAQPCSSASS NR41_RAT 72 20 -
LPGTVQPCSSASS NR41_HUMAN 71 19 -
LPGTTQPCSSACS NR41_MOUSE 71 19 -
LPGTAQPCSSASS NR41_CANFA 71 19 -

Motif 4 width=12
Element Seqn Id St Int Rpt
ATSPASASFKFE NR41_RAT 92 7 -
ATSPASASFKFE NR41_HUMAN 93 9 -
ATSPASASFKFE NR41_MOUSE 95 11 -
ATSPASASFKFE NR41_CANFA 93 9 -

Motif 5 width=20
Element Seqn Id St Int Rpt
PPTFFSFSPPTGPSPSLAQS NR41_RAT 185 81 -
PPAFFSFSPPTGPSPSLAQS NR41_HUMAN 186 81 -
PPTFFSFSPPTGPSPSLAQS NR41_MOUSE 189 82 -
PPAFFSFSPPTGPSPSLAQS NR41_CANFA 186 81 -

Motif 6 width=17
Element Seqn Id St Int Rpt
ATHQLGEGESYSVPAAF NR41_RAT 213 8 -
ATHQLGEGESYSMPTAF NR41_HUMAN 214 8 -
ATHQLGEGESYSMPAAF NR41_MOUSE 217 8 -
ATCQLGERESYSISTAF NR41_CANFA 214 8 -

Motif 7 width=16
Element Seqn Id St Int Rpt
GLAPTSPNCDTSGILD NR41_RAT 231 1 -
GLAPTSPHLEGSGILD NR41_HUMAN 232 1 -
GLAPTSPNRDTSGILD NR41_MOUSE 235 1 -
GLAPTSPHLDGPGMLD NR41_CANFA 232 1 -

Motif 8 width=15
Element Seqn Id St Int Rpt
KQPPDASPTNLLTSL NR41_RAT 353 106 -
KQPPDASPANLLTSL NR41_HUMAN 354 106 -
KQPPDASPTNLLTSL NR41_MOUSE 357 106 -
KQPPDASPANLLTSL NR41_CANFA 354 106 -

Motif 9 width=16
Element Seqn Id St Int Rpt
EHMAAVAGDPQPASCL NR41_RAT 536 168 -
EHVAAVAGEPQPASCL NR41_HUMAN 537 168 -
EHMATVAGDPQPASCL NR41_MOUSE 540 168 -
EHVSAVAGEPQPASCL NR41_CANFA 537 168 -