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[191509_at] Homeobox domain

Description Y75B8A.1 /REP_DB=WormBase Gene ID /WP=CE28148 /GEN=php-3 /TR=Q9XW88 /GB=CAA22081.2 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Homeobox domain
Cluster 6grp_total > 08      4grp_total > 13      6grp_cgc > 10      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 12
1 2 3 4 range
A 9.8
(0)
A 		7.9
(-1)
A 		3.8
(-3)
A 		15.8
(3)
A 		12
B 10.7
(2.7)
A 		7.2
(-0.2)
A 		11.1
(3)
A 		3.8
(-3)
A 		7
C 6.4
(-2.4)
A 		6.4
(-2.4)
A 		5.7
(-3)
A 		12.2
(3)
A 		7
avr 9
(0.4) 		7.2
(-2.5) 		6.9
(-3) 		10.6
(3) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 12
1 2 3 4 5 6 range
A 5.1
(-0.6)
A 		3.6
(-1.9)
A 		6.4
(0.4)
A 		9.6
(3)
A 		7
(0.9)
A 		2.2
(-3)
A 		7
B 4.4
(-1)
A 		2.8
(-3)
A 		4.1
(-1.4)
A 		3.8
(-1.8)
A 		3.3
(-2.4)
A 		7.7
(3)
A 		5
C 14
(3)
A 		8.1
(-0.3)
A 		8.7
(0)
A 		3.4
(-2.9)
A 		4.8
(-2.2)
A 		3.3
(-3)
A 		11
avr 7.8
(3) 		4.8
(-2.3) 		6.4
(0.5) 		5.6
(-0.9) 		5
(-1.9) 		4.4
(-3) 		3
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3
1 2 3 4 range
A 3.6
(3)
A 		1.7
(-1.4)
A 		1
(-3)
A 		2.3
(-0)
A 		3
B 3.4
(3)
A 		1.8
(-0.7)
A 		2.6
(1.2)
A 		0.8
(-3)
A 		3
C 2.1
(3)
A 		1.8
(-3)
A 		2
(1)
A 		2.1
(3)
A 		0
avr 3
(3) 		1.8
(-2.5) 		1.9
(-2.1) 		1.7
(-3) 		1

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5
1 2 3 4 5 6 range
A 0.9
(-1.7)
A 		1.3
(-0.5)
A 		1.4
(-0.2)
A 		2.4
(3)
A 		2.1
(2.1)
A 		0.5
(-3)
A 		2
B 1.5
(-1.2)
A 		0.9
(-3)
A 		1
(-2.7)
A 		1
(-2.7)
A 		1.3
(-1.8)
A 		2.9
(3)
A 		2
C 5.2
(3)
A 		2.5
(-0.6)
A 		2.2
(-1)
A 		0.7
(-3)
A 		1.6
(-1.8)
A 		1.1
(-2.5)
A 		5
avr 2.5
(3) 		1.6
(-1.9) 		1.5
(-2.5) 		1.4
(-3) 		1.7
(-1.4) 		1.5
(-2.5) 		1
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191509_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6131
Sequence Type Exemplar sequence
Representative Public ID Y75B8A.1 NCBI
Target Description Y75B8A.1 /REP_DB=WormBase Gene ID /WP=CE28148 /GEN=php-3 /TR=Q9XW88 /GB=CAA22081.2 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Homeobox domain
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_067172(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067172 NCBI Caenorhabditis elegans Posterior Hox gene Paralog family member (php-3) (php-3) mRNA, complete cds. 11/11 None
SNAP00000020063 ENSEMBL cdna:SNAP chromosome:CEL140:III:12074482:12077378:-1 11/11 None
GENEFINDER00000020184 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:12074482:12077339:-1 11/11 None
Y75B8A.1 ENSEMBL cdna:known chromosome:CEL140:III:12074166:12077432:-1 gene:Y75B8A.1 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:12074477-12077335(-) 100.0 100.0
Public Domain and Genome References
Gene Title Homeobox domain
Gene Symbol php-3
Ensembl Y75B8A.1
Entrez Gene 176640 Entrez gene
SwissProt Q9XW88 EMBL-EBI
WormBase CE28148 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA22081 Hypothetical protein Y75B8A.1 [Caenorhabditis elegans] ref|NP_499573.1| Posterior Hox gene Paralog family member (php-3) [Caenorhabditis elegans] gb|AAD48876.1| homeodomain protein PHP-3 [Caenorhabditis elegans] 1.0E-115
blast CAE75107 Hypothetical protein CBG23030 [Caenorhabditis briggsae] 2.0E-68
blast CAE75107 Hypothetical protein CBG23030 [Caenorhabditis briggsae] 4.0E-68
blast CAA33187 unnamed protein product [Drosophila melanogaster] gb|AAS65159.1| CG11648-PE, isoform E [Drosophila melanogaster] gb|AAN13723.1| CG11648-PD, isoform D [Drosophila melanogaster] gb|AAF55364.2| CG11648-PC, isoform C [Drosophila melanogaster] gb|AAF55363.1| CG11648-PA, isoform A [Drosophila melanogaster] ref|NP_996220.1| CG11648-PE, isoform E [Drosophila melanogaster] ref|NP_732181.1| CG11648-PD, isoform D [Drosophila melanogaster] ref|NP_732180.1| CG11648-PC, isoform C [Drosophila melanogaster] ref|NP_650577.1| CG11648-PA, isoform A [Drosophila melanogaster] gb|AAA84403.1| ABD-BII 8.0E-26
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 4.99999984132761E-20
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 5.99999980959314E-20
Pfam IPR001356 EMBL-EBI Homeobox 1.3E-28
Pfam IPR001356 EMBL-EBI Homeobox 1.3E-28
Sequence
Target Sequence 
>C. ELEGANS:191509_AT
cagcaatctgtatctggatcatctggtgtttctagtggttccagcagttctgcatcgaac
aatttatcaaggacacaagcggacaatcattcggaacgaggatccgacactgcttccagt
cctcaggttgcaccactcccaacgagcagtggtatgtcaatgccagcagcggctgcagcc
ggaatgtacccattcaatgctggtcgatttccaacagagtttaatatgatggttaatcaa
tcaatgtacaatgatttctattcaaatagtcttgctgcatcttcttggccatactcttat
ccacaacaatatccgtttgcaaactactcaatgccaagtttagatggaaatttgaatgac
ggtggtcaactagaatggacgtcctcttcacacgcaatgcgtaaaaagaggaagccgtat
acgaaagcgcagacattggagttggaaaaagagtttttgtacaatacctacgtcagtaag
cagaagcggtgggaacttgcaaagtacttgcatttgactgagcgaca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGCAATCTGTATCTGGATCATCTG 230 205 172 Antisense
CTAGTGGTTCCAGCAGTTCTGCATC 358 225 203 Antisense
GGAACGAGGATCCGACACTGCTTCC 638 527 264 Antisense
TGCACCACTCCCAACGAGCAGTGGT 101 579 300 Antisense
TATGTCAATGCCAGCAGCGGCTGCA 218 657 324 Antisense
AGCGGCTGCAGCCGGAATGTACCCA 426 81 339 Antisense
ATGTACCCATTCAATGCTGGTCGAT 70 49 355 Antisense
AATAGTCTTGCTGCATCTTCTTGGC 406 173 436 Antisense
TCTTGGCCATACTCTTATCCACAAC 632 617 454 Antisense
ACTAGAATGGACGTCCTCTTCACAC 329 99 540 Antisense
AGTACTTGCATTTGACTGAGCGACA 127 63 674 Antisense
Sequence Source Affymetrix Proprietary Database