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[193511_at] homeobox protein (NK-2 subfamily)

Description F55B12.1 /REP_DB=WormBase Gene ID /WP=CE25006 /GEN=ceh-24 /TR=Q9NLC2 /GB=CAB60999.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=homeobox protein (NK-2 subfamily)
Cluster 6grp_total > 15      4grp_total > 29      6grp_cgc > 21      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 106
1 2 3 4 range
A 108.3
(3)
A 		73.7
(-1.8)
A 		74.7
(-1.7)
A 		65.4
(-3)
A 		43
B 93
(2.1)
A 		106.1
(3)
A 		15.4
(-3)
A 		77.7
(1.1)
A 		91
C 115.3
(2.6)
A 		45.1
(-2.4)
A 		37.3
(-3)
A 		120.9
(3)
A 		84
avr 105.5
(3) 		75
(0.1) 		42.5
(-3) 		88
(1.3) 		63

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 142
1 2 3 4 5 6 range
A 113.8
(3)
A 		71.9
(0.3)
A 		76.2
(0.5)
A 		24.2
(-2.9)
A 		22.3
(-3)
A 		25.6
(-2.8)
A 		92
B 127.6
(3)
A 		79
(0.5)
A 		90.3
(1.1)
A 		53.5
(-0.8)
A 		10.3
(-3)
A 		35.9
(-1.7)
A 		117
C 151.8
(3)
A 		116.4
(1.5)
A 		53.6
(-1.3)
A 		65.2
(-0.7)
A 		66.1
(-0.7)
A 		13.2
(-3)
A 		139
avr 131.1
(3) 		89.1
(0.6) 		73.4
(-0.3) 		47.6
(-1.7) 		32.9
(-2.5) 		24.9
(-3) 		106
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 36
1 2 3 4 range
A 39.4
(3)
A 		16
(-1.7)
A 		19.5
(-1)
A 		9.6
(-3)
A 		30
B 29.7
(3)
A 		26.2
(2.2)
A 		3.6
(-3)
A 		16.6
(-0)
A 		26
C 38.2
(3)
A 		13
(-3)
A 		13
(-3)
A 		20.4
(-1.2)
A 		25
avr 35.8
(3) 		18.4
(-1.4) 		12
(-3) 		15.5
(-2.1) 		24

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 52
1 2 3 4 5 6 range
A 21
(1.6)
A 		25.6
(3)
A 		16.6
(0.2)
A 		6.1
(-3)
A 		6.7
(-2.8)
A 		6.2
(-3)
A 		20
B 44.4
(3)
A 		26.3
(0.3)
A 		21.9
(-0.4)
A 		14.2
(-1.5)
A 		4.2
(-3)
A 		13.4
(-1.6)
A 		40
C 56.3
(3)
A 		35.5
(0.6)
A 		13.6
(-1.9)
A 		13.1
(-2)
A 		21.4
(-1)
A 		4.4
(-3)
A 		52
avr 40.6
(3) 		29.1
(0.9) 		17.4
(-1.3) 		11.1
(-2.4) 		10.8
(-2.5) 		8
(-3) 		33
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193511_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13204
Sequence Type Exemplar sequence
Representative Public ID F55B12.1 NCBI
Target Description F55B12.1 /REP_DB=WormBase Gene ID /WP=CE25006 /GEN=ceh-24 /TR=Q9NLC2 /GB=CAB60999.1 /SUBMIT=HINXTON /CHR=5 /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_074018(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074018 NCBI Caenorhabditis elegans C.Elegans Homeobox family member (ceh-24) (ceh-24) mRNA, complete cds. 11/11 None
SNAP00000009638 ENSEMBL cdna:SNAP chromosome:CEL140:V:13815898:13817861:1 9/11 None
GENEFINDER00000009654 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:13815639:13817861:1 11/11 None
F55B12.1 ENSEMBL cdna:known chromosome:CEL140:V:13815829:13817937:1 gene:F55B12.1 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
chrV:13815897-13817861(+) 100.0 100.0
Public Domain and Genome References
Gene Title homeobox protein (NK-2 subfamily)
Gene Symbol ceh-24
Ensembl F55B12.1
Entrez Gene 179877 Entrez gene
SwissProt Q9NLC2 EMBL-EBI
WormBase CE25006 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 CAB60999 Hypothetical protein F55B12.1 [Caenorhabditis elegans] ref|NP_506419.3| C.Elegans Homeobox family member (ceh-24) [Caenorhabditis elegans] sp|Q9NLC2|HM24_CAEEL Homeobox protein ceh-24 1.0E-126
blast AAB81844 NK-2 class homeodomain protein; CEH-24 [Caenorhabditis elegans] 1.0E-124
blast CAB60999 Hypothetical protein F55B12.1 [Caenorhabditis elegans] ref|NP_506419.3| C.Elegans Homeobox family member (ceh-24) [Caenorhabditis elegans] sp|Q9NLC2|HM24_CAEEL Homeobox protein ceh-24 1.0E-124
blast AAB81844 NK-2 class homeodomain protein; CEH-24 [Caenorhabditis elegans] 1.0E-122
blast CAB60999 Hypothetical protein F55B12.1 [Caenorhabditis elegans] ref|NP_506419.3| C.Elegans Homeobox family member (ceh-24) [Caenorhabditis elegans] sp|Q9NLC2|HM24_CAEEL Homeobox protein ceh-24 1.0E-102
blast AAB81844 NK-2 class homeodomain protein; CEH-24 [Caenorhabditis elegans] 1.0E-100
blast O17319 Homeobox protein ceh-24 5.0E-82
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 1.99999999495049E-6
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 2.99999996001683E-24
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 7.00000013679037E-25
Pfam IPR001356 EMBL-EBI Homeobox 1.8E-26
Pfam IPR001356 EMBL-EBI Homeobox 1.4E-6
Pfam IPR001356 EMBL-EBI Homeobox 1.8E-26
Sequence
Target Sequence 
>C. ELEGANS:193511_AT
accatttcctggttacagcggagctcaaccaaattggtacaatgggaatgatccaagatt
tgcagcagctgcagctttacttccgtgctctattgatccagttagatctgctataaatca
tcaattttcaatgagttcaatgagtcaacgacggaaaagaagagtcctattcagtcaggc
acaagtttacgaattggaacgaagattcaaacaagcgaaatatttaactgctccggaaag
ggagcaactggctaattcgattcggttgactccaacgcaggtgaagatctggtttcaaaa
ccaccgatacaagtgcaagcgtcaggagaaagaaaaagcaatgagtggtcttggacacag
tgaagatggaagctcacccccaccagataacgatgatgatgacgacaaatactctattga
aatggatgataaagatgacgaggaggaagaagaatcagaaaaaccagtgttaaagccaag
tggagtatttgggctcccctaccctccaaatgctgctgcagctgccgccgctgcagcggc
tgcgttcaattttccttttgctgcacaag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACCATTTCCTGGTTACAGCGGAGCT 126 87 312 Antisense
ATGATCCAAGATTTGCAGCAGCTGC 438 43 359 Antisense
TACTTCCGTGCTCTATTGATCCAGT 126 645 389 Antisense
GAAGAGTCCTATTCAGTCAGGCACA 24 339 470 Antisense
GAGCAACTGGCTAATTCGATTCGGT 194 391 553 Antisense
TCGATTCGGTTGACTCCAACGCAGG 8 603 568 Antisense
AGTGAAGATGGAAGCTCACCCCCAC 136 61 670 Antisense
CACCCCCACCAGATAACGATGATGA 60 199 686 Antisense
CAAGTGGAGTATTTGGGCTCCCCTA 197 183 788 Antisense
GCTGCAGCGGCTGCGTTCAATTTTC 441 295 841 Antisense
TTCAATTTTCCTTTTGCTGCACAAG 372 685 856 Antisense
Sequence Source Affymetrix Proprietary Database