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[189665_at] Homeobox domain

Description R06F6.6 /REP_DB=WormBase Gene ID /WP=CE01622 /TR=SW:Q09602 /GB=CAA86776.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Homeobox domain
Cluster 6grp_highest_10_10 > 0      6grp_high1_10_10 > 0      4grp_high_8_8 > 33      6grp_highest_nonorm > 80      6grp_total > 04      4grp_total > 46      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 184
1 2 3 4 range
A 191.6
(3)
P 		146.6
(0.2)
P 		139.5
(-0.3)
P 		96.1
(-3)
A 		96
B 279.6
(3)
P 		157.3
(-1.4)
P 		125.1
(-2.5)
P 		111.2
(-3)
P 		168
C 274.5
(3)
P 		185.7
(-0.4)
P 		116.6
(-3)
M 		179.7
(-0.6)
P 		158
avr 248.6
(3) 		163.2
(-1.2) 		127.1
(-3) 		129
(-2.9) 		122

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 217
1 2 3 4 5 6 range
A 340
(3)
P 		260
(0.4)
P 		211.1
(-1.1)
P 		234.4
(-0.4)
P 		230.6
(-0.5)
P 		152.4
(-3)
P 		188
B 303.6
(3)
P 		192.2
(-1.1)
P 		174.5
(-1.8)
P 		278.6
(2.1)
P 		198.9
(-0.9)
P 		141.1
(-3)
P 		163
C 318.1
(3)
P 		266.3
(1.4)
P 		206.7
(-0.4)
P 		297.6
(2.4)
P 		202.9
(-0.5)
P 		123
(-3)
P 		195
avr 320.6
(3) 		239.5
(0.3) 		197.4
(-1.1) 		270.2
(1.3) 		210.8
(-0.6) 		138.8
(-3) 		182
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 77
1 2 3 4 range
A 69.8
(3)
P 		31.8
(-1.1)
P 		36.5
(-0.6)
P 		14.1
(-3)
A 		56
B 89.2
(3)
P 		38.8
(-1.6)
P 		29
(-2.5)
P 		23.7
(-3)
P 		66
C 90.9
(3)
P 		53.4
(-0.7)
P 		40.6
(-2)
M 		30.3
(-3)
P 		61
avr 83.3
(3) 		41.3
(-1.2) 		35.4
(-1.7) 		22.7
(-3) 		61

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 81
1 2 3 4 5 6 range
A 62.7
(-0.2)
P 		92.5
(3)
P 		46
(-2)
P 		59.5
(-0.6)
P 		69.6
(0.5)
P 		37.1
(-3)
P 		55
B 105.6
(3)
P 		64
(-0.9)
P 		42.4
(-3)
P 		73.8
(-0)
P 		80.8
(0.6)
P 		52.6
(-2)
P 		63
C 117.9
(3)
P 		81.3
(0.1)
P 		52.6
(-2.1)
P 		59.8
(-1.5)
P 		65.7
(-1.1)
P 		41.2
(-3)
P 		77
avr 95.4
(3) 		79.3
(1.1) 		47
(-2.6) 		64.4
(-0.6) 		72
(0.3) 		43.6
(-3) 		52
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189665_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3913
Sequence Type Exemplar sequence
Representative Public ID R06F6.6 NCBI
Target Description R06F6.6 /REP_DB=WormBase Gene ID /WP=CE01622 /TR=SW:Q09602 /GB=CAA86776.1 /SUBMIT=HINXTON /CHR=2 /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_063925(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063925 NCBI Caenorhabditis elegans R06F6.6 (R06F6.6) mRNA, complete cds. 11/11 None
R06F6.6 ENSEMBL cdna:known chromosome:CEL140:II:10805305:10809700:1 gene:R06F6.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000015431 5/11 Cross Hyb Matching Probes None
SNAP00000015432 3/11 Cross Hyb Matching Probes None
GENEFINDER00000015438 3/11 Cross Hyb Matching Probes None
GENEFINDER00000015442 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:10805301-10809697(+) 100.0 100.0
Public Domain and Genome References
Gene Title Homeobox domain
Ensembl R06F6.6
Entrez Gene 187642 Entrez gene
SwissProt Q09602 EMBL-EBI
WormBase CE01622 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 CAA86776 Hypothetical protein R06F6.6 [Caenorhabditis elegans] ref|NP_496326.1| R06F6.6 [Caenorhabditis elegans] sp|Q09602|YRM6_CAEEL Hypothetical homeobox protein R06F6.6 in chromosome II 1.0E-163
blast P18264 Homeobox protein rough gb|AAA28861.1| rough protein 5.0E-13
blast A30046 homeotic protein rough - fruit fly (Drosophila melanogaster) 9.0E-13
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 8.9999997143897E-21
Pfam IPR001356 EMBL-EBI Homeobox 2.0E-25
Sequence
Target Sequence 
>C. ELEGANS:189665_AT
ctcaaattcaaactgctagccctccaactaccgctgactctgcgatttttccaccgactt
ccccagaaagcattattcaaaaaattgagcagttcccaagcaatcagattcttcccaact
ttgatatccttcaaacttatttgcaatctttgtcaagctctcagatcccacttcaatttg
taccctcaactcctccattattcgacccaaatatgcttcagctttatcatgtcatttttg
aattctcgcaatccgaaacttgttcagtttcatttcaacgcaactcagctagcaacatga
gatcccttctcattttcgtcttttttgcaaccatttttgccgttgatgctcaatacgatt
cggccgactcatctcaatcggaagatcttccagatattgctccagaatccgtgtcttcag
aag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTCAAATTCAAACTGCTAGCCCTCC 343 227 695 Antisense
TACCGCTGACTCTGCGATTTTTCCA 606 649 723 Antisense
GAGCAGTTCCCAAGCAATCAGATTC 452 387 781 Antisense
ATCTTTGTCAAGCTCTCAGATCCCA 229 31 840 Antisense
TCAGATCCCACTTCAATTTGTACCC 669 621 855 Antisense
ATTCGACCCAAATATGCTTCAGCTT 507 9 894 Antisense
GTTTCATTTCAACGCAACTCAGCTA 460 449 961 Antisense
CAGCTAGCAACATGAGATCCCTTCT 134 205 980 Antisense
GTTGATGCTCAATACGATTCGGCCG 668 435 1036 Antisense
TTCGGCCGACTCATCTCAATCGGAA 311 695 1053 Antisense
GCTCCAGAATCCGTGTCTTCAGAAG 698 297 1093 Antisense
Sequence Source Affymetrix Proprietary Database