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[193479_at] homeobox protein (NK-2 subfamily)

Description K03A11.3 /REP_DB=WormBase Gene ID /WP=CE06073 /GEN=ceh-28 /TR=Q21169 /GB=CAB00867.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=homeobox protein (NK-2 subfamily)
Cluster 6grp_total > 43      4grp_total > 10      6grp_cgc > 80      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 57
1 2 3 4 range
A 6.6
(-0.6)
A 		11.8
(3)
A 		8.5
(0.7)
A 		3.2
(-3)
A 		9
B 3.6
(-3)
A 		8.6
(3)
A 		7
(1.1)
A 		4.5
(-1.9)
A 		5
C 7.4
(-2.7)
A 		4.8
(-3)
A 		5.5
(-2.9)
A 		60.3
(3)
A 		56
avr 5.9
(-3) 		8.4
(-2.1) 		7
(-2.6) 		22.7
(3) 		17

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 8
1 2 3 4 5 6 range
A 5.7
(-1.3)
A 		9.3
(1.6)
A 		11.1
(3)
A 		7.2
(-0.1)
A 		8.3
(0.8)
A 		3.5
(-3)
A 		8
B 6.9
(1.4)
A 		6.4
(0.9)
A 		8.3
(3)
A 		2.9
(-3)
A 		4.3
(-1.4)
A 		2.9
(-3)
A 		5
C 7.5
(1.3)
A 		7.3
(1.1)
A 		8.8
(3)
A 		4.1
(-3)
A 		8.2
(2.2)
A 		4.7
(-2.2)
A 		5
avr 6.7
(0.2) 		7.7
(1.2) 		9.4
(3) 		4.7
(-1.9) 		6.9
(0.4) 		3.7
(-3) 		6
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10
1 2 3 4 range
A 2.4
(2.4)
A 		2.6
(3)
A 		2.2
(1.9)
A 		0.5
(-3)
A 		2
B 1.1
(-2.5)
A 		2.1
(3)
A 		1.6
(0.3)
A 		1
(-3)
A 		1
C 2.4
(-2.3)
A 		1.4
(-3)
A 		1.9
(-2.7)
A 		10.2
(3)
A 		9
avr 2
(-2.7) 		2
(-2.7) 		1.9
(-3) 		3.9
(3) 		2

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3
1 2 3 4 5 6 range
A 1.1
(-2.3)
A 		3.3
(3)
A 		2.4
(0.8)
A 		1.8
(-0.6)
A 		2.5
(1.1)
A 		0.8
(-3)
A 		3
B 2.4
(3)
A 		2.1
(1.9)
A 		2
(1.5)
A 		0.8
(-3)
A 		1.8
(0.8)
A 		1.1
(-1.9)
A 		2
C 2.8
(3)
A 		2.2
(1.2)
A 		2.2
(1.2)
A 		0.8
(-3)
A 		2.6
(2.4)
A 		1.6
(-0.6)
A 		2
avr 2.1
(1.3) 		2.5
(3) 		2.2
(1.7) 		1.1
(-3) 		2.3
(2.1) 		1.2
(-2.6) 		1
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193479_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17812
Sequence Type Exemplar sequence
Representative Public ID K03A11.3 NCBI
Target Description K03A11.3 /REP_DB=WormBase Gene ID /WP=CE06073 /GEN=ceh-28 /TR=Q21169 /GB=CAB00867.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=homeobox protein (NK-2 subfamily)
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_077768(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077768 NCBI Caenorhabditis elegans C.Elegans Homeobox family member (ceh-28) (ceh-28) mRNA, complete cds. 10/11 None
K03A11.3 ENSEMBL cdna:known chromosome:CEL140:X:13074602:13075713:1 gene:K03A11.3 10/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000007881 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:13074601-13075713(+) 96.77 100.0
Public Domain and Genome References
Gene Title homeobox protein (NK-2 subfamily)
Gene Symbol ceh-28
Ensembl K03A11.3
Entrez Gene 191619 Entrez gene
SwissProt Q21169 EMBL-EBI
WormBase CE34047 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 CAB00867 Hypothetical protein K03A11.3 [Caenorhabditis elegans] ref|NP_510169.2| C.Elegans Homeobox family member (ceh-28) [Caenorhabditis elegans] 1.0E-107
blast AAO46042 NK-2 family homeodomain factor CEH-28; K03A11.3 [Caenorhabditis elegans] 1.0E-85
blast CAE61378 Hypothetical protein CBG05223 [Caenorhabditis briggsae] 3.0E-68
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 5.00000022906852E-19
Pfam IPR001356 EMBL-EBI Homeobox 6.6E-29
Sequence
Target Sequence 
>C. ELEGANS:193479_AT
accaagtgaagtgatccaaccgccacagcaatctgcagttccttcagagtttaaaaatac
acttccgtcgcgtttaaatctatttgaaggttttgatcagtcattttctgaacttacaaa
tccatatcaaccagttattccgttgatgcagagagaatccttgttaggtgcaagttcata
ttatagtgagttcaatcgatatttatttaaaataaaagcttgtttgaaaaaccatttgat
gatttcaggttctccaagtcaaaatcagagatcttatcagaatcaccgtcaacattctaa
tccagatactatcaatctgagatcacaacagcagaagagaaaaccgagagttttgttcac
acaacatcaggttaatgaacttgaagaacgatttaaaaagcaacgttatgtgacagccac
tgagcgagaagagctagcccaatgtcttggcctcacagccacacaagtgaaaatttggtt
tcaaaatcgccgatacaaatgcaagcggttagcccaggacagaaccttacaattgagcca
gatccctttcaatccagtgagtttaattttcctttcacgagag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACCAAGTGAAGTGATCCAACCGCCA 667 81 51 Antisense
CCACAGCAATCTGCAGTTCCTTCAG 248 275 73 Antisense
TACACTTCCGTCGCGTTTAAATCTA 284 625 108 Antisense
AATCCATATCAACCAGTTATTCCGT 587 167 169 Antisense
GATGATTTCAGGTTCTCCAAGTCAA 658 409 288 Antisense
ATCACCGTCAACATTCTAATCCAGA 588 27 332 Antisense
AAGAGCTAGCCCAATGTCTTGGCCT 179 155 479 Antisense
AATGCAAGCGGTTAGCCCAGGACAG 273 165 548 Antisense
GAACCTTACAATTGAGCCAGATCCC 95 347 572 Antisense
CAGATCCCTTTCAATCCAGTGAGTT 664 205 589 Antisense
GAGTTTAATTTTCCTTTCACGAGAG 55 397 609 Antisense
Sequence Source Affymetrix Proprietary Database