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[189806_at] 'Paired box' domain

Description C09G9.7 /REP_DB=WormBase Gene ID /WP=CE03006 /TR=Q17876 /GB=CAA90976.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Paired box domain
Cluster 6grp_total > 93      4grp_total > 50      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 81
1 2 3 4 range
A 28.4
(3)
A 		16.2
(-0.2)
A 		7.7
(-2.4)
A 		5.4
(-3)
A 		23
B 33.6
(-3)
A 		45.9
(0.6)
A 		54.3
(3)
A 		49.5
(1.6)
A 		21
C 10.6
(-2.5)
A 		84
(3)
A 		55
(0.8)
A 		3.4
(-3)
A 		81
avr 24.2
(-2) 		48.7
(3) 		39
(1) 		19.4
(-3) 		29

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 40
1 2 3 4 5 6 range
A 11.8
(-1)
A 		4.7
(-3)
A 		14.7
(-0.2)
A 		4.8
(-3)
A 		26.2
(3)
A 		7.1
(-2.3)
A 		22
B 10.2
(-1.6)
A 		20.9
(0.5)
A 		33.7
(3)
A 		3.2
(-3)
A 		22
(0.7)
A 		5.4
(-2.6)
A 		31
C 9.8
(-2.1)
A 		12.2
(-1.7)
A 		10.9
(-1.9)
A 		3.6
(-3)
A 		42.8
(3)
A 		7.2
(-2.4)
A 		39
avr 10.6
(-1.5) 		12.6
(-1) 		19.8
(0.6) 		3.9
(-3) 		30.3
(3) 		6.6
(-2.4) 		26
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 24
1 2 3 4 range
A 10.3
(3)
A 		3.5
(-1.3)
A 		2
(-2.2)
A 		0.8
(-3)
A 		10
B 10.7
(-2.4)
A 		11.3
(-0.7)
A 		12.6
(3)
A 		10.5
(-3)
A 		2
C 3.5
(-2.3)
A 		24.2
(3)
A 		19.2
(1.7)
A 		0.6
(-3)
A 		24
avr 8.2
(-0.2) 		13
(3) 		11.3
(1.9) 		4
(-3) 		9

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 13
1 2 3 4 5 6 range
A 2.2
(-2.1)
A 		1.7
(-2.6)
A 		3.2
(-1.2)
A 		1.2
(-3)
A 		7.9
(3)
A 		1.7
(-2.6)
A 		7
B 3.5
(-1.1)
A 		7
(1.6)
A 		8.2
(2.5)
A 		0.9
(-3)
A 		8.9
(3)
A 		2
(-2.2)
A 		8
C 3.6
(-1.7)
A 		3.7
(-1.6)
A 		2.8
(-2)
A 		0.7
(-3)
A 		13.9
(3)
A 		2.4
(-2.2)
A 		13
avr 3.1
(-1.6) 		4.1
(-0.9) 		4.7
(-0.5) 		0.9
(-3) 		10.2
(3) 		2
(-2.3) 		9
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189806_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9713
Sequence Type Exemplar sequence
Representative Public ID C09G9.7 NCBI
Target Description C09G9.7 /REP_DB=WormBase Gene ID /WP=CE03006 /TR=Q17876 /GB=CAA90976.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Paired box 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_069139(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069139 NCBI Caenorhabditis elegans C09G9.7 (C09G9.7) mRNA, complete cds. 11/11 None
SNAP00000008791 ENSEMBL cdna:SNAP chromosome:CEL140:IV:8878974:8879804:-1 11/11 None
GENEFINDER00000008796 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:8877535:8879807:-1 11/11 None
C09G9.7 ENSEMBL cdna:known chromosome:CEL140:IV:8879180:8879804:-1 gene:C09G9.7 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
chrIV:8879185-8879810(-) 100.0 100.0
Public Domain and Genome References
Gene Title 'Paired box' domain
Ensembl C09G9.7
Entrez Gene 182466 Entrez gene
SwissProt Q17876 EMBL-EBI
WormBase CE03006 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
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
Protein Similarities
Method ID Description E-Value
blast CAA90976 Hypothetical protein C09G9.7 [Caenorhabditis elegans] ref|NP_501540.1| C09G9.7 [Caenorhabditis elegans] 1.0E-68
blast CAA90976 Hypothetical protein C09G9.7 [Caenorhabditis elegans] ref|NP_501540.1| C09G9.7 [Caenorhabditis elegans] 5.0E-68
blast CAA90976 Hypothetical protein C09G9.7 [Caenorhabditis elegans] ref|NP_501540.1| C09G9.7 [Caenorhabditis elegans] 4.0E-65
blast CAE73598 Hypothetical protein CBG21083 [Caenorhabditis briggsae] 1.0E-59
blast CAE73598 Hypothetical protein CBG21083 [Caenorhabditis briggsae] 5.0E-59
blast CAE73598 Hypothetical protein CBG21083 [Caenorhabditis briggsae] 5.0E-56
blast CAE67597 Hypothetical protein CBG13139 [Caenorhabditis briggsae] 1.0E-11
Protein Domains
Database ID Description E-Value
scop a.4.1.Paired domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Paired domain 8.99999968283527E-24
scop a.4.1.Paired domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Paired domain 7.99999974612418E-20
scop a.4.1.Paired domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Paired domain 1.00000001686238E-16
Pfam IPR001523 EMBL-EBI Paired box protein, N-terminal 7.6E-9
Pfam IPR001523 EMBL-EBI Paired box protein, N-terminal 9.0E-5
Pfam IPR001523 EMBL-EBI Paired box protein, N-terminal 5.5E-13
Sequence
Target Sequence 
>C. ELEGANS:189806_AT
atgtcgccatcaatatttccaccgatcaacttcctttttcaaaactctgctctgctctct
agctttgctgcacaaaaagctttgtcaaatggtcatccatcaggttcgtcacttgctgca
ttggaaaaactatcaaaagcgttccggcgaccggatcttcatattgaaaagcttgcttcg
tcatgcattgataagcaaaaggatttgaaaatgaccaatgtggtcccatcacgaaatcga
tatggtcggccatacatctctgggcgaccacttctaacttgtgat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGTCGCCATCAATATTTCCACCGA 695 47 13 Antisense
ACTTCCTTTTTCAAAACTCTGCTCT 135 105 41 Antisense
GCTCTCTAGCTTTGCTGCACAAAAA 343 299 66 Antisense
AAATGGTCATCCATCAGGTTCGTCA 506 119 99 Antisense
AGGTTCGTCACTTGCTGCATTGGAA 684 55 114 Antisense
ATCAAAAGCGTTCCGGCGACCGGAT 299 25 144 Antisense
GTTCCGGCGACCGGATCTTCATATT 617 441 153 Antisense
AAAGCTTGCTTCGTCATGCATTGAT 431 123 180 Antisense
GACCAATGTGGTCCCATCACGAAAT 613 381 225 Antisense
GATATGGTCGGCCATACATCTCTGG 331 425 251 Antisense
TGGGCGACCACTTCTAACTTGTGAT 184 555 273 Antisense
Sequence Source Affymetrix Proprietary Database