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[189172_s_at] Homeobox domain

Description C49C3.5 /REP_DB=WormBase Gene ID /WP=CE19744 /TR=Q9XUG3 /GB=CAB05155.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Homeobox domain
Cluster 6grp_total > 20      4grp_total > 05      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 313
1 2 3 4 range
A 283.2
(-1.2)
A 		214.1
(-3)
A 		223.9
(-2.7)
A 		439.6
(3)
A 		226
B 315.6
(1.3)
A 		196.4
(-2.1)
A 		165.8
(-3)
A 		376.9
(3)
A 		211
C 286.8
(-1)
A 		189.1
(-3)
A 		206
(-2.7)
A 		479.2
(3)
A 		290
avr 295.2
(-0.5) 		199.9
(-3) 		198.6
(-3) 		431.9
(3) 		233

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 196
1 2 3 4 5 6 range
A 242.3
(-3)
A 		350
(2.6)
A 		357.3
(3)
A 		338.9
(2)
A 		297.9
(-0.1)
A 		247.8
(-2.7)
A 		115
B 337.5
(-0.3)
A 		358.8
(1)
A 		390.9
(3)
A 		384.9
(2.6)
A 		294.8
(-3)
A 		324.2
(-1.2)
A 		96
C 277.1
(-3)
A 		416.4
(2.2)
A 		345.9
(-0.4)
A 		292
(-2.4)
A 		281.7
(-2.8)
A 		438.2
(3)
A 		161
avr 285.6
(-3) 		375.1
(3) 		364.7
(2.3) 		338.6
(0.6) 		291.5
(-2.6) 		336.7
(0.4) 		90
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 65
1 2 3 4 range
A 103.1
(3)
A 		46.5
(-3)
A 		58.5
(-1.7)
A 		64.4
(-1.1)
A 		57
B 100.6
(3)
A 		48.5
(-2)
A 		38.4
(-3)
A 		80.3
(1)
A 		62
C 94.9
(3)
A 		54.4
(-3)
A 		71.8
(-0.4)
A 		80.8
(0.9)
A 		41
avr 99.5
(3) 		49.8
(-3) 		56.2
(-2.2) 		75.2
(0.1) 		50

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 102
1 2 3 4 5 6 range
A 44.7
(-3)
A 		124.5
(3)
A 		77.8
(-0.5)
A 		86
(0.1)
A 		89.9
(0.4)
A 		60.3
(-1.8)
A 		80
B 117.4
(2.2)
A 		119.4
(2.7)
A 		94.9
(-3)
A 		101.9
(-1.4)
A 		119.8
(2.7)
A 		120.9
(3)
A 		26
C 102.7
(0)
A 		127.1
(1.7)
A 		88
(-1)
A 		58.7
(-3)
A 		91.1
(-0.8)
A 		146.7
(3)
A 		88
avr 88.3
(-2.1) 		123.7
(3) 		86.9
(-2.3) 		82.2
(-3) 		100.3
(-0.4) 		109.3
(0.9) 		42
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189172_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8670
Sequence Type Exemplar sequence
Representative Public ID C49C3.5 NCBI
Target Description C49C3.5 /REP_DB=WormBase Gene ID /WP=CE19744 /TR=Q9XUG3 /GB=CAB05155.1 /SUBMIT=HINXTON /CHR=4 /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_070680(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070680 NCBI Caenorhabditis elegans C49C3.5 (C49C3.5) mRNA, complete cds. 11/11 None
GENEFINDER00000040212 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:17329160:17331345:1 11/11 None
C49C3.5 ENSEMBL cdna:known chromosome:CEL140:IV:17329160:17331345:1 gene:C49C3.5 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000040195 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:17329165-17331351(+) 100.0 100.0
Public Domain and Genome References
Gene Title Homeobox domain
Ensembl C49C3.5
Entrez Gene 178514 Entrez gene
SwissProt Q9XUG3 EMBL-EBI
WormBase CE19744 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 CAB05155 Hypothetical protein C49C3.5 [Caenorhabditis elegans] ref|NP_503081.1| C49C3.5 [Caenorhabditis elegans] 1.0E-153
blast CAE61222 Hypothetical protein CBG05017 [Caenorhabditis briggsae] 2.0E-58
blast CAE57525 Hypothetical protein CBG00500 [Caenorhabditis briggsae] 2.0E-52
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 6.5
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.00300000002607703
Pfam IPR001356 EMBL-EBI Homeobox 8.6E-7
Sequence
Target Sequence 
>C. ELEGANS:189172_S_AT
cccgccacccaagcaaatgtatgagttcacaagtgaacaacggggtgctctggatcaagc
gtttctcgttacacctcaaatggattcagatggtgcaagggagttatcagaaattactgg
cttaactgtgaagcagatcaacaactggttttgcaatcaacgccgtaaagctgatggacg
aagtgcggagaaagacaagaaacgaagggagcggattcgagaagacatgaaaaagaacgg
cttagggagagtcggaacttttcgatctgaagctgtggaactttttgagaaggagtacga
gactatgttgcaactagaggcgattggtggaggaaaagttcgaattccatatacggaatt
agtggagaaaactggaatggagaggaagaagattcgtgattggttctcgaagcgaaaagg
aagagacaagcggttcttggagaatatggagaatactcgtgaagtttctccgcaaaatac
gcagcaaaatattcaagatattttgattaaaattgtgactcaaaaagaggaaagtgcgct
ccagcgtcatgcaccagagatgagagacgcgggacaacgagacggatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCCGCCACCCAAGCAAATGTATGAG 141 261 249 Antisense
AGTGAACAACGGGGTGCTCTGGATC 57 59 280 Antisense
TGCTCTGGATCAAGCGTTTCTCGTT 558 579 294 Antisense
GTTTCTCGTTACACCTCAAATGGAT 597 449 309 Antisense
GAGTCGGAACTTTTCGATCTGAAGC 321 399 497 Antisense
GGAGTACGAGACTATGTTGCAACTA 49 515 540 Antisense
GAATACTCGTGAAGTTTCTCCGCAA 616 325 699 Antisense
GTTTCTCCGCAAAATACGCAGCAAA 80 451 712 Antisense
AGAGGAAAGTGCGCTCCAGCGTCAT 355 65 774 Antisense
CTCCAGCGTCATGCACCAGAGATGA 110 237 787 Antisense
GAGACGCGGGACAACGAGACGGATT 350 393 812 Antisense
Sequence Source Affymetrix Proprietary Database