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PR01256

Identifier
OTX1HOMEOBOX  [View Relations]  [View Alignment]  
Accession
PR01256
No. of Motifs
3
Creation Date
06-DEC-1999
Title
Otx1 transcription factor signature
Database References
PRINTS; PR01255 OTXHOMEOBOX
PRODOM; PD012033
INTERPRO; IPR003026
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.
 
Studies of mice lacking Otx1 (due to targeted gene disruption) have shed
light on its role in development, such mice showing impaired corticogenesis
and sense organ development. Phenotypic abnormalities noted in the cerebral 
cortices include reduced cell proliferation and total cell number, together
with disruption of the formation of the normally well-ordered cortical cell
layers, which are characteristic of these structures. Abnormalities are also
observed in the eye and inner ear.
 
OTX1HOMEOBOX is a 3-element fingerprint that provides a signature for the 
Otx1 transcription factor. The fingerprint was derived from an initial 
alignment of 3 sequences: the motifs were drawn from conserved regions 
within the C-terminal half of the alignment, focusing on those sections that
characterise Otx1 but distinguish it from other Otx isoforms - motif 1 lies
after the homeobox DNA-binding domain; motif 2 encodes a portion of the
histidine-rich region of the sequence; and motif 3 lies after this. Two
iterations on SPTR37_10f were required to reach convergence, at which point
a true set comprising 4 sequences was identified. 
Summary Information
4 codes involving  3 elements
0 codes involving 2 elements
Composite Feature Index
3444
2000
123
True Positives
OTX1_BRARE    OTX1_HUMAN    OTX1_MOUSE    OTX1_RAT      
Sequence Titles
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).
Scan History
SPTR37_10f 2  300  NSINGLE    
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
PGSAPASVSVPEP OTX1_HUMAN 184 184 -
PGSAPTSVSVPEP OTX1_MOUSE 184 184 -
PGSAPPSVSLPEP OTX1_BRARE 170 170 -

Motif 2 width=13
Element Seqn Id St Int Rpt
LSQSSGHHHHHHH OTX1_HUMAN 286 89 -
LSQSSGHHHHHHH OTX1_MOUSE 286 89 -
ISQSSGHHHHHHH OTX1_BRARE 262 79 -

Motif 3 width=6
Element Seqn Id St Int Rpt
GSGLAF OTX1_HUMAN 306 7 -
GSGLAF OTX1_MOUSE 307 8 -
GTGLAF OTX1_BRARE 279 4 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
PGSAPASVSVPEP OTX1_HUMAN 184 184 -
PGSAPASVSVPEP OTX1_RAT 184 184 -
PGSAPTSVSVPEP OTX1_MOUSE 184 184 -
PGSAPPSVSLPEP OTX1_BRARE 170 170 -

Motif 2 width=13
Element Seqn Id St Int Rpt
LSQSSGHHHHHHH OTX1_HUMAN 286 89 -
LSQSSGHHHHHHH OTX1_RAT 286 89 -
LSQSSGHHHHHHH OTX1_MOUSE 286 89 -
ISQSSGHHHHHHH OTX1_BRARE 262 79 -

Motif 3 width=6
Element Seqn Id St Int Rpt
GSGLAF OTX1_HUMAN 306 7 -
GSGLAF OTX1_RAT 307 8 -
GSGLAF OTX1_MOUSE 307 8 -
GTGLAF OTX1_BRARE 279 4 -