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[192900_at] 'Paired box' domain, Homeobox domain

Description Y53C12C.1 /REP_DB=WormBase Gene ID /WP=CE14906 /TR=O01996 /GB=CAB09133.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Paired box domain, Homeobox domain
Cluster 6grp_total > 45      4grp_total > 15      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 96
1 2 3 4 range
A 104.9
(3)
A 		8.5
(-3)
A 		15.3
(-2.6)
A 		59.3
(0.2)
A 		96
B 68.1
(3)
A 		16.4
(-3)
A 		65.2
(2.7)
A 		37.5
(-0.6)
A 		52
C 54.2
(-0.4)
A 		26.8
(-2.9)
A 		25.5
(-3)
A 		91.3
(3)
A 		66
avr 75.7
(3) 		17.2
(-3) 		35.3
(-1.1) 		62.7
(1.7) 		59

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 75
1 2 3 4 5 6 range
A 61.6
(1.7)
A 		62.5
(1.9)
A 		59.8
(1.4)
A 		42.9
(-2)
A 		67.8
(3)
A 		38.2
(-3)
A 		30
B 43.4
(-0.3)
A 		78.3
(3)
A 		74.1
(2.6)
A 		22.7
(-2.2)
A 		13.9
(-3)
A 		38.4
(-0.7)
A 		64
C 26
(-0.7)
A 		50.8
(1.9)
A 		14.2
(-1.9)
A 		30.3
(-0.2)
A 		3.7
(-3)
A 		60.8
(3)
A 		57
avr 43.7
(-0.4) 		63.9
(3) 		49.4
(0.5) 		32
(-2.4) 		28.5
(-3) 		45.8
(-0.1) 		35
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 36
1 2 3 4 range
A 38.2
(3)
A 		1.8
(-3)
A 		4
(-2.6)
A 		8.7
(-1.9)
A 		36
B 21.7
(3)
A 		4.1
(-3)
A 		15.1
(0.8)
A 		8
(-1.7)
A 		18
C 17.9
(3)
A 		7.7
(-3)
A 		8.9
(-2.3)
A 		15.4
(1.5)
A 		10
avr 25.9
(3) 		4.5
(-3) 		9.3
(-1.7) 		10.7
(-1.3) 		21

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 25
1 2 3 4 5 6 range
A 11.3
(-2.1)
A 		22.2
(3)
A 		13
(-1.3)
A 		10.9
(-2.3)
A 		20.4
(2.2)
A 		9.3
(-3)
A 		13
B 15.1
(-0.2)
A 		26.1
(3)
A 		18
(0.6)
A 		6
(-2.9)
A 		5.7
(-3)
A 		14.3
(-0.5)
A 		20
C 9.6
(-0.4)
A 		15.5
(1.5)
A 		3.6
(-2.3)
A 		6.1
(-1.5)
A 		1.2
(-3)
A 		20.4
(3)
A 		19
avr 12
(-1.1) 		21.3
(3) 		11.5
(-1.3) 		7.7
(-3) 		9.1
(-2.4) 		14.7
(0.1) 		14
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192900_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3234
Sequence Type Exemplar sequence
Representative Public ID Y53C12C.1 NCBI
Target Description Y53C12C.1 /REP_DB=WormBase Gene ID /WP=CE14906 /TR=O01996 /GB=CAB09133.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Paired box domain, 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_063715(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063715 NCBI Caenorhabditis elegans Y53C12C.1 (Y53C12C.1) mRNA, complete cds. 11/11 None
SNAP00000025826 ENSEMBL cdna:SNAP chromosome:CEL140:II:9826424:9827705:-1 11/11 None
GENEFINDER00000025828 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:9826424:9827837:-1 11/11 None
Y53C12C.1 ENSEMBL cdna:known chromosome:CEL140:II:9826424:9827837:-1 gene:Y53C12C.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
chrII:9826420-9827834(-) 100.0 100.0
Public Domain and Genome References
Gene Title 'Paired box' domain, Homeobox domain
Ensembl Y53C12C.1
Entrez Gene 190204 Entrez gene
SwissProt O01996 EMBL-EBI
WormBase CE14906 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
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 CAB09133 Hypothetical protein Y53C12C.1 [Caenorhabditis elegans] ref|NP_496116.1| Y53C12C.1 [Caenorhabditis elegans] 1.0E-133
blast CAB09133 Hypothetical protein Y53C12C.1 [Caenorhabditis elegans] ref|NP_496116.1| Y53C12C.1 [Caenorhabditis elegans] 1.0E-118
blast CAE57965 Hypothetical protein CBG01026 [Caenorhabditis briggsae] 1.0E-104
blast CAE57965 Hypothetical protein CBG01026 [Caenorhabditis briggsae] 4.0E-90
blast XP_394294 PREDICTED: similar to CG10488-PA, isoform A [Apis mellifera] 2.0E-29
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 5.99999980959314E-20
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 4.99999984132761E-20
scop a.4.1.Paired domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Paired domain 4.00000012549758E-22
scop a.4.1.Paired domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Paired domain 1.99999993653105E-21
Pfam IPR001523 EMBL-EBI Paired box protein, N-terminal 3.5E-26
Pfam IPR001356 EMBL-EBI Homeobox 8.6E-27
Pfam IPR001523 EMBL-EBI Paired box protein, N-terminal 3.5E-26
Pfam IPR001356 EMBL-EBI Homeobox 8.6E-27
Sequence
Target Sequence 
>C. ELEGANS:192900_AT
ggagcttcaaatgatcctttcggctcaacatctagctcgtccgcgtgctcaacaagtccg
actgcctcctgcatttccattcccattcccattggtttggcctggactgttaccaaatcc
tgctcagctgtcgttgctattgaactcaggagcgttggctccgcctgttcagtcaggagg
agcaggaggtcctggagtttttggaaattctgggcaaatatcggtagactcgaatctgaa
tttgtcggaagacgactcaactcttggcgcaaatgctagaagactctcgaggagtacttt
tacaaatgaacaactacaaagtctggaagaagtcttcctccgcgatccctacccatctcc
caatgaacgagctgatcttgtcaagagaaccaatttgccagaagcacgtatacaagtctg
gttttcaaatcgtcgtgcaaaatggcgaaagacaaatgcaaatggaagtgatcgagatga
attgagagctgaacgatctgaaacagatgatgctttaagtatttccagtcagtcaccatc
acctggaggaggac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAGCTTCAAATGATCCTTTCGGCT 192 521 342 Antisense
CATTCCCATTGGTTTGGCCTGGACT 441 217 425 Antisense
GACTGTTACCAAATCCTGCTCAGCT 298 375 446 Antisense
CTGCTCAGCTGTCGTTGCTATTGAA 626 237 461 Antisense
TGAACTCAGGAGCGTTGGCTCCGCC 242 571 482 Antisense
GCTCCGCCTGTTCAGTCAGGAGGAG 472 297 499 Antisense
GACTCAACTCTTGGCGCAAATGCTA 402 373 595 Antisense
CTGGAAGAAGTCTTCCTCCGCGATC 248 241 664 Antisense
CTACCCATCTCCCAATGAACGAGCT 351 225 690 Antisense
TAAGTATTTCCAGTCAGTCACCATC 567 637 857 Antisense
CAGTCACCATCACCTGGAGGAGGAC 632 207 871 Antisense
Sequence Source Affymetrix Proprietary Database