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PR01255

Identifier
OTXHOMEOBOX  [View Relations]  [View Alignment]  
Accession
PR01255
No. of Motifs
4
Creation Date
06-DEC-1999
Title
Otx transcription factor signature
Database References
PRINTS; PR01256 OTX1HOMEOBOX; PR01257 OTX2HOMEOBOX
PRODOM; PD004529; PD005982; PD007122
INTERPRO; IPR003025
Literature References
1. ACAMPORA, D. AND SIMEONE, A.
Understanding the roles of Otx1 and Otx2 in the control of brain
morphogenesis.
TRENDS NEUROSCIENCE 22 116-122 (1999).
 
2. HIRTH, F. AND REICHERT, H.
Conserved genetic programs in insect and mammalian brain development.
BIOESSAYS 21 677-684 (1999).
 
3. KLEIN, W.H. AND LI, X.
Function and evolution of Otx proteins.
BIOCHEM.BIOPHYS.RES.COMMUN. 258 229-233 (1999).

Documentation
Otx proteins constitute a class of vertebrate homeodomain-containing
transcription factors that have been shown to be essential for anterior
head formation, including brain morphogenesis. They are orthologous to the
product of the Drosophila head gap gene, orthodenticle (Otd), and appear to
play similar roles in both, since the developmental abnormalities caused by
disruption of these transcription factors in one, can be recovered by
substitution of the factor(s) from the other. Such studies have provided
strong evidence that there exists a conserved genetic programme for insect
and mammalian brain development, which presumably arose in a more primitive
common ancestor [1,2].
 
Two vertebrate orthodenticle-related transcription factors have been
indentified, Otx1 and Otx2, which have sizes of 355 and 289 residues
respectively. They contain a bicoid-like homeodomain, which features a
conserved lysine residue at position 9 of the DNA recognition helix, which
is thought to confer high-affinity binding to TAATCC/T elements on DNA [3].
Otd-like transcription factors have also been found in zebrafish and 
certain lamprey species.
 
OTXHOMEOBOX is a 4-element fingerprint that provides a signature for Otx
transcription factors. The fingerprint was derived from an initial
alignment of 7 sequences: the motifs were drawn from conserved regions
spanning virtually the full alignment length - motif 1 enocodes the first
10 residues of the N-terminus (prior to the homeobox DNA-binding domain);
and motifs 2-4 encode short stretches (7-9 residues) of the C-terminal half
of the sequence alignment. Two iterations on SPTR37_10f were required to
reach convergence, at which point a true set comprising 10 sequences was
identified. A single partial match was also found, Q9YHDO, a sea lamprey 
Otx protein that matches motifs 1 and 4.
Summary Information
  10 codes involving  4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
410101010
30000
21001
1234
True Positives
O93488        OTX1_BRARE    OTX1_HUMAN    OTX1_MOUSE    
OTX1_RAT OTX2_BRARE OTX2_HUMAN OTX2_MOUSE
OTX2_XENLA OTX3_BRARE
True Positive Partials
Codes involving 2 elements
Q9YHD0
Sequence Titles
O93488      LJOTXA - LAMPETRA JAPONICA (JAPANESE LAMPREY). 
OTX1_BRARE HOMEOBOX PROTEIN OTX1 (ZOTX1) - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
OTX1_HUMAN HOMEOBOX PROTEIN OTX1 - HOMO SAPIENS (HUMAN).
OTX1_MOUSE HOMEOBOX PROTEIN OTX1 - MUS MUSCULUS (MOUSE).
OTX1_RAT HOMEOBOX PROTEIN OTX1 - RATTUS NORVEGICUS (RAT).
OTX2_BRARE HOMEOBOX PROTEIN OTX2 (ZOTX2) - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
OTX2_HUMAN HOMEOBOX PROTEIN OTX2 - HOMO SAPIENS (HUMAN).
OTX2_MOUSE HOMEOBOX PROTEIN OTX2 - MUS MUSCULUS (MOUSE).
OTX2_XENLA HOMEOBOX PROTEIN OTX2 (XOTX2) (ORTHODENTICLE 2) - XENOPUS LAEVIS (AFRICAN CLAWED
OTX3_BRARE HOMEOBOX PROTEIN OTX3 (ZOTX3) - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).

Q9YHD0 OTX - PETROMYZON MARINUS (SEA LAMPREY).
Scan History
SPTR37_10f 2  100  NSINGLE    
Initial Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
MMSYLKQAPY OTX3_BRARE 1 1 -
MMSYLKQPPY OTX1_BRARE 1 1 -
MMSYLKQPPY OTX2_XENLA 1 1 -
MMSYLKQPPY OTX2_MOUSE 1 1 -
MMSYLKQPPY OTX2_HUMAN 1 1 -
MMSYLKQPPY OTX1_HUMAN 1 1 -
MMSYLKQPPY OTX1_MOUSE 1 1 -

Motif 2 width=7
Element Seqn Id St Int Rpt
YPMSYGQ OTX1_MOUSE 221 210 -
YPMPYNQ OTX1_BRARE 203 192 -
YPMTYTQ OTX2_XENLA 175 164 -
YPMTYTQ OTX2_MOUSE 175 164 -
YPMTYTQ OTX2_HUMAN 175 164 -
YPMSYGQ OTX1_HUMAN 221 210 -
YPMPYNQ OTX3_BRARE 212 201 -

Motif 3 width=9
Element Seqn Id St Int Rpt
YFGGMDCGS OTX2_XENLA 195 13 -
YFGGMDCGS OTX2_MOUSE 195 13 -
YFGGMDCGS OTX2_HUMAN 195 13 -
YFGGVDCSS OTX1_HUMAN 242 14 -
YFGGVDCSS OTX1_MOUSE 242 14 -
YFGGMDCGS OTX3_BRARE 234 15 -
YFSGVDCGS OTX1_BRARE 224 14 -

Motif 4 width=7
Element Seqn Id St Int Rpt
DCLDYKD OTX2_XENLA 254 50 -
DCLDYKD OTX2_MOUSE 255 51 -
DCLDYKD OTX2_HUMAN 255 51 -
DCLDYKE OTX1_HUMAN 315 64 -
DCLDYKE OTX1_MOUSE 316 65 -
DCLDYKE OTX3_BRARE 301 58 -
DCLDYKE OTX1_BRARE 288 55 -
Final Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
MMSYLKQPPY OTX1_RAT 1 1 -
MMSYLKQAPY OTX3_BRARE 1 1 -
MMSYLKQPPY OTX1_BRARE 1 1 -
MMSYLKQSPY O93488 1 1 -
MMSYLKQPPY OTX2_BRARE 1 1 -
MMSYLKQPPY OTX2_XENLA 1 1 -
MMSYLKQPPY OTX2_MOUSE 1 1 -
MMSYLKQPPY OTX2_HUMAN 1 1 -
MMSYLKQPPY OTX1_HUMAN 1 1 -
MMSYLKQPPY OTX1_MOUSE 1 1 -

Motif 2 width=7
Element Seqn Id St Int Rpt
YPMSYGQ OTX1_MOUSE 221 210 -
YPMPYNQ OTX3_BRARE 212 201 -
YPMPYNQ OTX1_BRARE 203 192 -
YAMTYSQ O93488 175 164 -
YPMTYTQ OTX2_BRARE 175 164 -
YPMTYTQ OTX2_XENLA 175 164 -
YPMTYTQ OTX2_MOUSE 175 164 -
YPMTYTQ OTX2_HUMAN 175 164 -
YPMSYGQ OTX1_HUMAN 221 210 -
YPMSYGQ OTX1_RAT 221 210 -

Motif 3 width=9
Element Seqn Id St Int Rpt
YFGGMDCGS OTX2_BRARE 195 13 -
YFGGMDCGS OTX2_XENLA 195 13 -
YFGGMDCGS OTX2_MOUSE 195 13 -
YFGGMDCGS OTX2_HUMAN 195 13 -
YFGGVDCSS OTX1_HUMAN 242 14 -
YFGGVDCSS OTX1_MOUSE 242 14 -
YFGGVDCSS OTX1_RAT 242 14 -
YFGGMDCGS OTX3_BRARE 234 15 -
YFSGVDCGS OTX1_BRARE 224 14 -
YFGGVDCGS O93488 198 16 -

Motif 4 width=7
Element Seqn Id St Int Rpt
DCLDYKD OTX2_BRARE 255 51 -
DCLDYKD OTX2_XENLA 254 50 -
DCLDYKD OTX2_MOUSE 255 51 -
DCLDYKD OTX2_HUMAN 255 51 -
DCLDYKE OTX1_HUMAN 315 64 -
DCLDYKE OTX1_MOUSE 316 65 -
DCLDYKE OTX1_RAT 316 65 -
DCLDYKE OTX3_BRARE 301 58 -
DCLDYKE OTX1_BRARE 288 55 -
DCLDYKE O93488 262 55 -