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[193866_at] 'Paired box' domain, homeobox protein (paired subfamily)

Description F27E5.2 /REP_DB=WormBase Gene ID /WP=CE01563 /TR=Q09546 /GB=CAA88702.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Paired box domain, homeobox protein (paired subfamily)
Cluster 6grp_total > 17      4grp_total > 31      6grp_cgc > 11      6grp_cgc_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 89
1 2 3 4 range
A 92.7
(3)
A 		3.8
(-3)
A 		13.4
(-2.4)
A 		49.5
(0.1)
A 		89
B 62.5
(3)
A 		5.7
(-3)
A 		6.2
(-2.9)
A 		40.3
(0.7)
A 		57
C 62.4
(3)
A 		10
(-2.6)
A 		10.4
(-2.5)
A 		5.9
(-3)
A 		57
avr 72.5
(3) 		6.5
(-3) 		10
(-2.7) 		31.9
(-0.7) 		66

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 74
1 2 3 4 5 6 range
A 60
(3)
A 		8.3
(-2.8)
A 		35.2
(0.2)
A 		9.8
(-2.7)
A 		6.9
(-3)
A 		19
(-1.6)
A 		53
B 61.3
(3)
A 		28.7
(-1)
A 		31.5
(-0.7)
A 		12.5
(-3)
A 		30.4
(-0.8)
A 		17.2
(-2.4)
A 		49
C 80.9
(3)
P 		35.8
(-0.8)
A 		38.2
(-0.6)
A 		36.5
(-0.7)
A 		9.7
(-3)
A 		39.5
(-0.5)
A 		71
avr 67.4
(3) 		24.3
(-2) 		35
(-0.8) 		19.6
(-2.5) 		15.7
(-3) 		25.2
(-1.9) 		52
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 33
1 2 3 4 range
A 33.7
(3)
A 		0.8
(-3)
A 		3.5
(-2.5)
A 		7.2
(-1.8)
A 		33
B 19.9
(3)
A 		1.4
(-3)
A 		1.4
(-3)
A 		8.6
(-0.7)
A 		19
C 20.7
(3)
A 		2.9
(-2.4)
A 		3.6
(-2.2)
A 		1
(-3)
A 		20
avr 24.8
(3) 		1.7
(-3) 		2.8
(-2.7) 		5.6
(-2) 		23

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 28
1 2 3 4 5 6 range
A 11.1
(3)
A 		2.9
(-2.5)
A 		7.7
(0.7)
A 		2.5
(-2.7)
A 		2.1
(-3)
A 		4.6
(-1.3)
A 		9
B 21.3
(3)
A 		9.6
(-0.9)
A 		7.6
(-1.6)
A 		3.3
(-3)
A 		12.3
(0)
A 		6.4
(-2)
A 		18
C 30
(3)
P 		10.9
(-1.3)
A 		9.7
(-1.5)
A 		7.3
(-2.1)
A 		3.1
(-3)
A 		13.2
(-0.7)
A 		27
avr 20.8
(3) 		7.8
(-1.8) 		8.3
(-1.6) 		4.4
(-3) 		5.8
(-2.5) 		8.1
(-1.6) 		16
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193866_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2612
Sequence Type Exemplar sequence
Representative Public ID F27E5.2 NCBI
Target Description F27E5.2 /REP_DB=WormBase Gene ID /WP=CE01563 /TR=Q09546 /GB=CAA88702.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Paired box domain, homeobox protein (paired subfamily)
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_063788(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063788 NCBI Caenorhabditis elegans PAX (Paired box) transcription factor family member (pax-3) (pax-3) mRNA, complete cds. 10/11 None
SNAP00000027282 ENSEMBL cdna:SNAP chromosome:CEL140:II:10151806:10152356:1 10/11 None
GENEFINDER00000027295 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10151309:10152436:1 11/11 None
F27E5.2 ENSEMBL cdna:known chromosome:CEL140:II:10146759:10152356:1 gene:F27E5.2 10/11 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
chrII:10146755-10152433(+) 100.0 100.0
Public Domain and Genome References
Gene Title 'Paired box' domain, homeobox protein (paired subfamily)
Gene Symbol pax-3
Ensembl F27E5.2
Entrez Gene 185022 Entrez gene
SwissProt Q09546 EMBL-EBI
WormBase CE35862 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1637031_AT gooseberry-neuro dm
DROSGENOME1:143182_AT gooseberry-neuro dm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
7275 development 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 CAA88702 Hypothetical protein F27E5.2 [Caenorhabditis elegans] emb|CAA88468.2| Hypothetical protein F27E5.2 [Caenorhabditis elegans] ref|NP_496189.2| PAX (Paired box) transcription factor family member (pax-3) [Caenorhabditis elegans] 1.0E-136
blast CAE57834 Hypothetical protein CBG00861 [Caenorhabditis briggsae] 1.0E-103
blast CAA88702 Hypothetical protein F27E5.2 [Caenorhabditis elegans] emb|CAA88468.2| Hypothetical protein F27E5.2 [Caenorhabditis elegans] ref|NP_496189.2| PAX (Paired box) transcription factor family member (pax-3) [Caenorhabditis elegans] 7.0E-49
blast AAH76069 Pax3 protein [Danio rerio] 5.0E-44
blast CAA88702 Hypothetical protein F27E5.2 [Caenorhabditis elegans] emb|CAA88468.2| Hypothetical protein F27E5.2 [Caenorhabditis elegans] ref|NP_496189.2| PAX (Paired box) transcription factor family member (pax-3) [Caenorhabditis elegans] 3.0E-39
blast CAE57834 Hypothetical protein CBG00861 [Caenorhabditis briggsae] 7.0E-36
blast CAE57834 Hypothetical protein CBG00861 [Caenorhabditis briggsae] 3.0E-27
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 5.00000022906852E-19
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999968265523E-20
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999968265523E-21
scop a.4.1.Paired domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Paired domain 2.00000003908296E-25
scop a.4.1.Paired domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Paired domain 9.99999974737875E-5
Pfam IPR001523 EMBL-EBI Paired box protein, N-terminal 9.8E-54
Pfam IPR001356 EMBL-EBI Homeobox 8.1E-26
Pfam IPR001356 EMBL-EBI Homeobox 8.1E-26
Pfam IPR001356 EMBL-EBI Homeobox 8.1E-26
Sequence
Target Sequence 
>C. ELEGANS:193866_AT
cgaagagggctcttcaccatcaaacgacgcatcgtctcgtcgaaatcgtacatcattcac
tgccgagcaactagatgttcttgaaaatgcgttccgcgcagacacttacccacatgccaa
cgccagagagagcatttccaaggagacagggctcagcgaagagaaaattatgacgtggtt
ttcgaatcggcgagcaagatgtcggaaaaatatgccaatgtatcaacagtacaatgttca
aggttttggatcatctccgccggttatcctacccaacgctgctgccttcaccgatgatgt
tcctaccctcctactcaacgagtcctcaattgaatccgttattctttcaacacatactcc
aatcaagtcccccatcaagtcaatcatctccgccatcatcaagctaaacgct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGAAGAGGGCTCTTCACCATCAAAC 569 253 537 Antisense
ACGCATCGTCTCGTCGAAATCGTAC 389 91 563 Antisense
CGAAATCGTACATCATTCACTGCCG 176 253 577 Antisense
CACTGCCGAGCAACTAGATGTTCTT 154 199 594 Antisense
GAAAATGCGTTCCGCGCAGACACTT 619 353 619 Antisense
CCCACATGCCAACGCCAGAGAGAGC 62 259 645 Antisense
GACGTGGTTTTCGAATCGGCGAGCA 518 377 708 Antisense
TTCAAGGTTTTGGATCATCTCCGCC 512 685 773 Antisense
GAGTCCTCAATTGAATCCGTTATTC 681 399 856 Antisense
GTTATTCTTTCAACACATACTCCAA 28 449 874 Antisense
CTCCGCCATCATCAAGCTAAACGCT 237 235 924 Antisense
Sequence Source Affymetrix Proprietary Database