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[192273_at] paired box transcription factor

Description K06B9.5 /REP_DB=WormBase Gene ID /WP=CE07343 /TR=Q21263 /GB=AAA93452.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=paired box transcription factor
Cluster 6grp_total > 57      4grp_total > 18      6grp_cgc > 37      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 52
1 2 3 4 range
A 10.2
(-3)
A 		23
(-1.4)
A 		10.4
(-3)
A 		57.6
(3)
A 		47
B 10.8
(-2)
A 		16.3
(-0.7)
A 		6.1
(-3)
A 		33
(3)
A 		27
C 8.5
(-2.7)
A 		21.7
(3)
A 		7.9
(-3)
A 		17.2
(1)
A 		14
avr 9.8
(-2.6) 		20.3
(-0.4) 		8.1
(-3) 		35.9
(3) 		28

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 53
1 2 3 4 5 6 range
A 29.9
(3)
A 		5.8
(-3)
A 		25.5
(1.9)
A 		11.5
(-1.6)
A 		19
(0.3)
A 		6
(-3)
A 		24
B 13.6
(2.7)
A 		14
(3)
A 		8.8
(-0.9)
A 		8.7
(-0.9)
A 		8.2
(-1.3)
A 		5.9
(-3)
A 		8
C 9.1
(-2.5)
A 		15.7
(-1.7)
A 		13.7
(-2)
A 		26.5
(-0.5)
A 		4.6
(-3)
A 		57.3
(3)
A 		53
avr 17.5
(0.3) 		11.8
(-2.4) 		16
(-0.4) 		15.6
(-0.6) 		10.6
(-3) 		23.1
(3) 		13
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7
1 2 3 4 range
A 3.7
(-1.9)
A 		5
(-0.6)
A 		2.7
(-3)
A 		8.4
(3)
A 		6
B 3.5
(-0.8)
A 		4
(-0.2)
A 		1.4
(-3)
A 		7
(3)
A 		6
C 2.8
(-2.8)
A 		6.2
(3)
A 		2.7
(-3)
A 		2.9
(-2.7)
A 		4
avr 3.3
(-1.4) 		5.1
(1.4) 		2.3
(-3) 		6.1
(3) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 18
1 2 3 4 5 6 range
A 5.5
(2.7)
A 		2.1
(-2.1)
A 		5.6
(2.9)
A 		2.9
(-1)
A 		5.7
(3)
A 		1.5
(-3)
A 		4
B 4.7
(3)
A 		4.7
(3)
A 		2.1
(-3)
A 		2.3
(-2.5)
A 		3.3
(-0.2)
A 		2.2
(-2.8)
A 		3
C 3.4
(-2.4)
A 		4.8
(-1.9)
A 		3.5
(-2.3)
A 		5.3
(-1.7)
A 		1.5
(-3)
A 		19.2
(3)
A 		18
avr 4.5
(-1.5) 		3.9
(-2.4) 		3.7
(-2.7) 		3.5
(-3) 		3.5
(-3) 		7.6
(3) 		4
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192273_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11239
Sequence Type Exemplar sequence
Representative Public ID K06B9.5 NCBI
Target Description K06B9.5 /REP_DB=WormBase Gene ID /WP=CE07343 /TR=Q21263 /GB=AAA93452.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=paired box transcription factor
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_068112
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
GENEFINDER00000011545 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4199658:4204368:-1 None
NM_068112 NCBI Caenorhabditis elegans PAX (Paired box) transcription factor family member (pax-2) (pax-2) mRNA, complete cds. None
K06B9.5 ENSEMBL cdna:known chromosome:CEL140:IV:4199658:4204368:-1 gene:K06B9.5 None
SNAP00000011537 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4199658:4201909:-1 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:4201358-4202732(-) 96.7 100.0
Public Domain and Genome References
Gene Title paired box transcription factor
Gene Symbol pax-2
Ensembl K06B9.5
Entrez Gene 187062 Entrez gene
SwissProt Q21263 EMBL-EBI
WormBase CE29504 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 AAA93452 Pax (paired box) transcription factor protein 2 [Caenorhabditis elegans] ref|NP_500513.1| PAX (Paired box) transcription factor family member (pax-2) [Caenorhabditis elegans] 0.0
blast CAA94671 Hypothetical protein C04G2.7 [Caenorhabditis elegans] ref|NP_501836.1| EGg Laying defective family member (egl-38) [Caenorhabditis elegans] gb|AAC27976.1| PAX protein [Caenorhabditis elegans] 1.0E-127
blast CAA94671 Hypothetical protein C04G2.7 [Caenorhabditis elegans] ref|NP_501836.1| EGg Laying defective family member (egl-38) [Caenorhabditis elegans] gb|AAC27976.1| PAX protein [Caenorhabditis elegans] 1.0E-121
blast CAE67901 Hypothetical protein CBG13498 [Caenorhabditis briggsae] 1.0E-113
blast CAE67901 Hypothetical protein CBG13498 [Caenorhabditis briggsae] 1.0E-107
blast AAA93452 Pax (paired box) transcription factor protein 2 [Caenorhabditis elegans] ref|NP_500513.1| PAX (Paired box) transcription factor family member (pax-2) [Caenorhabditis elegans] 2.0E-95
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 2.0000000544904E-27
scop a.4.1.Paired domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Paired domain 9.00000005261382E-27
scop a.4.1.Paired domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Paired domain 1.0000000272452E-27
Pfam IPR001523 EMBL-EBI Paired box protein, N-terminal 2.5E-79
Pfam IPR001523 EMBL-EBI Paired box protein, N-terminal 2.9E-29
Pfam IPR001523 EMBL-EBI Paired box protein, N-terminal 1.4E-40
Pfam IPR001523 EMBL-EBI Paired box protein, N-terminal 2.9E-29
Sequence
Target Sequence 
>C. ELEGANS:192273_AT
ttctataaattcttccgcctcaaagatttttaattttcgtacttttcacgtttatcccac
gaagaaatttttgtgtaaaaatcccctactgtcagatggttcccacacgggcgttaatca
gttgggcggtgtattcgtcaacgggcggcctcttcctgacacaattcgtgctcaaatagt
cgaaatgtcacaacatggtacacggccgtgtgacatatcgagacagttgaaagtctccca
tggatgcgtttcaaaaatcctcggtcgatattattcaacaggatctgtcagaccaggagt
aattggaggctcaaagccaaaagttgccactccacgagtcgtggaatgtattgctggata
taaaagagcaaatccgacaatgttcgcatgggaaatacgacagaaattgattgaggacca
aatttgcggagaagaaaatgtgccatcagtgtcttcaattaatcgaattgtacggaataa
ggtaataatcttaaaggtggacagtgggaactcttcatcta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCTATAAATTCTTCCGCCTCAAAG 279 689 21 Antisense
TCGTACTTTTCACGTTTATCCCACG 271 605 57 Antisense
TTGTGTAAAAATCCCCTACTGTCAG 21 709 91 Antisense
ATGGTTCCCACACGGGCGTTAATCA 384 51 116 Antisense
AATCAGTTGGGCGGTGTATTCGTCA 42 171 136 Antisense
CTCTTCCTGACACAATTCGTGCTCA 9 231 170 Antisense
CACGGCCGTGTGACATATCGAGACA 448 199 221 Antisense
AGTCTCCCATGGATGCGTTTCAAAA 644 61 252 Antisense
GCGTTTCAAAAATCCTCGGTCGATA 114 289 266 Antisense
AAATGTGCCATCAGTGTCTTCAATT 272 121 456 Antisense
GTGGACAGTGGGAACTCTTCATCTA 8 491 517 Antisense
Sequence Source Affymetrix Proprietary Database