| Literature References | 1. XUE, Z.G., GEHRING, W.J. AND LE DOURAIN, N.M.
Quox-1, A quail homeobox gene expressed in the embryonic central nervous
system, including the forebrain.
PROC.NATL.ACAD.SCI.U.S.A. 88(6) 2427-2431 (1991).
2. GEHRING, W.J.
Homeo boxes in the study of development.
SCIENCE 236 1245-1252 (1987).
3. ANGERER, L.M., DOLECKI, G.J., GAGNON, M.L., LUM, R., WANG, G., YANG, Q.,
HUMPHREYS, T. AND ANGERER, R.C.
Progressively restricted expression of a homeo box gene within the aboral
ectoderm of developing sea urchin embryos.
GENES DEV. 3(3) 370-383 (1989).
4. SASAKI, H., YOKOYAMA, E. AND KUROIWA, A.
Specific DNA-binding of the 2 chicken deformed fmily homeodomain proteins,
Chox-1.4 AND Chox-A.
NUCLEIC ACIDS RES. 18 1739-1747 (1990).
5. BRENNAN, R.G., TAKEDA, Y., KIM, J., ANDERSON, W.F. AND MATTHEWS, B.W.
Crystallization of a complex of cro repressor with a 17 base pair operator.
J.MOL.BIOL. 188 115-118 (1986).
|
| Documentation | Organisms develop according to a precise program that specifies the body
plan in intricate detail and also determines the timing of developmental
events [1]. The highly complex nature of these events has suggested that
the process may be regulated by proteins capable of controlling the
temporal and spatial expression of many structural genes. The genes for
this process were first discovered as homeotic mutations in Drosophila [2],
and many similar genes are now known in a wide variety of organisms.
Proteins that regulate developmental gene expression are nuclear proteins
[3] that contain a conserved domain known as the homeobox, the flanking
sequences of which differ considerably among different proteins. The homeo
domain includes the helix-turn-helix (HTH) motif, which binds to DNA in a
sequence specific manner to exert a temporal and spatial regulation of
developmental gene expression [4]. The second helix of the HTH motif binds
to DNA via a number of hydrogen bonds and hydrophobic interactions, which
occur between specific side chains and the exposed bases and thymine methyl
groups within the major groove. The first helix may help to stablise the
structure [5].
Many homeodomain-containing proteins have now been sequenced and, while
the homeodomain flanking regions vary, characteristic conserved sequences
upstream of the domain allow the proteins to be grouped into 3 subfamilies:
the so-called antennapedia, engrailed and `paired box' proteins. The paired
box is a conserved 124 amino acid N-terminal domain of unknown function.
This usually, but not always, precedes a homeobox domain. Paired box genes
are expressed in alternate segments of the developing fruit fly, the
observed grouping of segments into pairs depending on the position of the
segment in the segmental array, and not on the identity of the segment as
in the case of homeotic genes. This implies that the genes affect different
processes from those altered by homeotic genes.
PAIREDBOX is a 4-element fingerprint that provides a signature for the
paired box domain. The fingerprint was derived from an initial alignment
of 6 sequences: the motifs span the first 80 residues of the domain,
2 and 3 including the region encoded by PROSITE pattern PAIRED_BOX
(PS00034). Two iterations on OWL20.0 were required to reach convergence,
at which point a true set comprising 23 sequences was identified.
An update on SPTR37_9f identified a true set of 89 sequences, and 1
partial match.
|
| Sequence Titles | GSBD_DROME GOOSEBERRY DISTAL PROTEIN (BSH9) - DROSOPHILA MELANOGASTER (FRUIT FLY).
GSBP_DROME GOOSEBERRY PROXIMAL PROTEIN (BSH4) - DROSOPHILA MELANOGASTER (FRUIT FLY).
HMPR_DROME SEGMENTATION PROTEIN PAIRED - DROSOPHILA MELANOGASTER (FRUIT FLY).
O02015 PAX-A - HYDRA LITTORALIS.
O02016 PAX-B - HYDRA LITTORALIS.
O16117 SPARKLING PROTEIN - DROSOPHILA MELANOGASTER (FRUIT FLY).
O16800 PAIRED BOX PROTEIN - PARACENTROTUS LIVIDUS (COMMON SEA URCHIN).
O16801 PAIRED BOX PROTEIN - PARACENTROTUS LIVIDUS (COMMON SEA URCHIN).
O16802 PAIRED BOX PROTEIN - STRONGYLOCENTROTUS PURPURATUS (PURPLE SEA URCHIN).
O18381 PAIRED BOX PROTEIN PAX-6 (EY) - DROSOPHILA MELANOGASTER (FRUIT FLY).
O42292 PAX-6 PROTEIN - ASTYANAX FASCIATUS (BLIND CAVE FISH) (ASTYANAX MEXICANUS).
O42293 PAX-6 PROTEIN - ASTYANAX FASCIATUS (BLIND CAVE FISH) (ASTYANAX MEXICANUS).
O42348 PAX6 PROTEIN - GALLUS GALLUS (CHICKEN).
O42349 PAX7 PROTEIN - GALLUS GALLUS (CHICKEN).
O42612 PAX-6 PROTEIN - ASTYANAX FASCIATUS (BLIND CAVE FISH) (ASTYANAX MEXICANUS).
O57416 TRANSCRIPTION FACTOR PAX3 - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
O57417 TRANSCRIPTION FACTOR PAX7A - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
O57418 TRANSCRIPTION FACTOR PAX7C - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
O57419 TRANSCRIPTION FACTOR PAX7D - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
O57420 TRANSCRIPTION FACTOR PAX7E - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
O57581 PAX6 LS - CYNOPS PYRRHOGASTER (JAPANESE COMMON NEWT).
O57582 PAX6 SS - CYNOPS PYRRHOGASTER (JAPANESE COMMON NEWT).
O57583 PAX6 LL - CYNOPS PYRRHOGASTER (JAPANESE COMMON NEWT).
O57584 PAX6 SL - CYNOPS PYRRHOGASTER (JAPANESE COMMON NEWT).
O57676 PAIRED BOX PROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O57677 PAIRED BOX PROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O57678 PAIRED BOX GENE - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O57679 PAIRED BOX PROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O57680 PAIRED BOX PROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O57681 PAIRED BOX PROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O57682 PAIRED BOX PROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O57684 PAIRED BOX PROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O57685 PAIRED BOX PROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O61616 PAIRED BOX PROTEIN PAX-2 ALPHA ISOFORM - BRANCHIOSTOMA FLORIDAE (FLORIDA LANCELET) (AMPHIOXUS).
O61617 PAIRED BOX PROTEIN PAX-2 BETA ISOFORM - BRANCHIOSTOMA FLORIDAE (FLORIDA LANCELET) (AMPHIOXUS).
O61988 PAX6 GENE (AMPHIPAX6) CLONE 12.1 (AMPHIPAX6) - BRANCHIOSTOMA FLORIDAE (FLORIDA LANCELET) (AMPHIOXUS).
O61990 PAX6 GENE (AMPHIPAX6), CLONE 4.1 - BRANCHIOSTOMA FLORIDAE (FLORIDA LANCELET) (AMPHIOXUS).
O61991 PAX6 GENE (AMPHIPAX6), CLONE 4.2 - BRANCHIOSTOMA FLORIDAE (FLORIDA LANCELET) (AMPHIOXUS).
O61992 PAX6 GENE (AMPHIPAX6), CLONE 12.2 - BRANCHIOSTOMA FLORIDAE (FLORIDA LANCELET) (AMPHIOXUS).
O76121 HRPAX-258 PROTEIN - HALOCYNTHIA RORETZI (SEA SQUIRT).
O88436 PAX4A - RATTUS NORVEGICUS (RAT).
O88437 PAX4B - RATTUS NORVEGICUS (RAT).
O88438 PAX4C - RATTUS NORVEGICUS (RAT).
O88439 PAX4D - RATTUS NORVEGICUS (RAT).
O93370 TRANSCRIPTION FACTOR - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
O93373 TRANSCRIPTION FACTOR - FUGU RUBRIPES (JAPANESE PUFFERFISH) (TAKIFUGU RUBRIPES).
P70053 PAX-6 - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
P91739 PAX-37 - HALOCYNTHIA RORETZI (SEA SQUIRT).
P91751 PAX-6 - LOLIGO OPALESCENS (CALIFORNIA MARKET SQUID).
P91781 PAX-6 - PHALLUSIA MAMMILATA.
PAX1_MOUSE PAIRED BOX PROTEIN PAX-1 - MUS MUSCULUS (MOUSE).
PAX2_BRARE PAIRED BOX PROTEIN PAX[ZF-B] (PAX-2) - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
PAX2_HUMAN PAIRED BOX PROTEIN PAX-2 - HOMO SAPIENS (HUMAN).
PAX2_MOUSE PAIRED BOX PROTEIN PAX-2 - MUS MUSCULUS (MOUSE).
PAX3_HUMAN PAIRED BOX PROTEIN PAX-3 (HUP2) - HOMO SAPIENS (HUMAN).
PAX3_MOUSE PAIRED BOX PROTEIN PAX-3 - MUS MUSCULUS (MOUSE).
PAX4_HUMAN PAIRED BOX PROTEIN PAX-4 - HOMO SAPIENS (HUMAN).
PAX5_HUMAN PAIRED BOX PROTEIN PAX-5 (B-CELL SPECIFIC TRANSCRIPTION FACTOR) (BSAP) - HOMO SAPIENS (HUMAN).
PAX5_MOUSE PAIRED BOX PROTEIN PAX-5 (B-CELL SPECIFIC TRANSCRIPTION FACTOR) (BSAP) - MUS MUSCULUS (MOUSE).
PAX6_BRARE PAIRED BOX PROTEIN PAX[ZF-A] (PAX-6) - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
PAX6_COTJA PAIRED BOX PROTEIN PAX-6 (PAX-QNR) - COTURNIX COTURNIX JAPONICA (JAPANESE QUAIL).
PAX6_HUMAN PAIRED BOX PROTEIN PAX-6 (OCULORHOMBIN) (ANIRIDIA, TYPE II PROTEIN) - HOMO SAPIENS (HUMAN).
PAX6_MOUSE PAIRED BOX PROTEIN PAX-6 - MUS MUSCULUS (MOUSE).
PAX6_ORYLA PAIRED BOX PROTEIN PAX-6 - ORYZIAS LATIPES (MEDAKA FISH).
PAX6_RAT PAIRED BOX PROTEIN PAX-6 - RATTUS NORVEGICUS (RAT).
PAX6_XENLA PAIRED BOX PROTEIN PAX-6 - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
PAX7_HUMAN PAIRED BOX PROTEIN PAX-7 (HUP1) - HOMO SAPIENS (HUMAN).
PAX8_MOUSE PAIRED BOX PROTEIN PAX-8 - MUS MUSCULUS (MOUSE).
PAX8_RAT PAIRED BOX PROTEIN PAX-8 - RATTUS NORVEGICUS (RAT).
PAX9_MOUSE PAIRED BOX PROTEIN PAX-9 - MUS MUSCULUS (MOUSE).
POXN_DROME PAIRED BOX POX-NEURO PROTEIN - DROSOPHILA MELANOGASTER (FRUIT FLY).
PX8A_CANFA PAIRED BOX PROTEIN PAX-8, ISOFORM 8A - CANIS FAMILIARIS (DOG).
PX8A_HUMAN PAIRED BOX PROTEIN PAX-8, ISOFORMS 8A/8B - HOMO SAPIENS (HUMAN).
PX8D_HUMAN PAIRED BOX PROTEIN PAX-8, ISOFORMS 8C/8D - HOMO SAPIENS (HUMAN).
PX8G_CANFA PAIRED BOX PROTEIN PAX-8, ISOFORM 8G - CANIS FAMILIARIS (DOG).
Q09546 HYPOTHETICAL 37.0 KD PROTEIN F27E5.2 IN CHROMOSOME II - CAENORHABDITIS ELEGANS.
Q12785 PAX3 PROTEIN-FORKHEAD TRANSCRIPTION FACTOR FUSION - HOMO SAPIENS (HUMAN).
Q16339 PAX8 - HOMO SAPIENS (HUMAN).
Q17132 AMPHIPAX-1 - BRANCHIOSTOMA FLORIDAE (FLORIDA LANCELET) (AMPHIOXUS).
Q17359 VARIABLE ABNORMAL-3 - CAENORHABDITIS ELEGANS.
Q17627 C04G2.7 - CAENORHABDITIS ELEGANS.
Q19466 VAB-3 PROTEIN - CAENORHABDITIS ELEGANS.
Q21263 SIMILAR TO PAIRED BOX TRANSCRIPTION FACTOR. NCBI GI: 1208883 - CAENORHABDITIS ELEGANS.
Q21272 SIMILARITY TO PAIRED BOX TRANSCRIPTION FACTORS - CAENORHABDITIS ELEGANS.
Q25411 PAX6-LIKE PROTEIN - LINEUS SANGUINEUS (RIBBON WORM).
Q26046 PAX-6 - PARACENTROTUS LIVIDUS (COMMON SEA URCHIN).
Q91886 PAIRED-TYPE HOMEODOMAIN PAX-6 PROTEIN (XPAX6) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
Q98865 PAX9A - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
Q98866 PAX9B - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANIO).
O61989 PAX6 GENE (AMPHIPAX6), CLONE J2 - BRANCHIOSTOMA FLORIDAE (FLORIDA LANCELET) (AMPHIOXUS).
|