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[192317_at] homeobox protein (NK-2 subfamily)

Description F46F3.1 /REP_DB=WormBase Gene ID /WP=CE10586 /TR=Q9XVN4 /GB=CAB03112.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=homeobox protein (NK-2 subfamily)
Cluster 6grp_highest_10_10 > 43      6grp_high1_10_10 > 13      4grp_highest_8_8 > 52      4grp_high_8_8 > 16      6grp_highest_nonorm > 90      6grp_total > 12      4grp_total > 39      6grp_highest_sub > 02      6grp_cgc > 43      6grp_high1_sub > De      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 129
1 2 3 4 range
A 202.9
(3)
P 		132.9
(-2.4)
P 		125.1
(-3)
P 		193.5
(2.3)
P 		78
B 246.9
(3)
P 		129.2
(-2.6)
P 		120.7
(-3)
P 		162
(-1)
P 		126
C 249.9
(3)
P 		150.3
(-1.8)
P 		125.5
(-3)
P 		158.2
(-1.4)
P 		124
avr 233.2
(3) 		137.5
(-2.2) 		123.8
(-3) 		171.2
(-0.4) 		109

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 122
1 2 3 4 5 6 range
A 143.9
(0.3)
P 		181.2
(3)
P 		123.8
(-1.1)
P 		144.8
(0.4)
P 		97.6
(-3)
P 		98.2
(-3)
P 		84
B 128.4
(-1.7)
P 		210.7
(3)
P 		182.7
(1.4)
P 		143.1
(-0.8)
P 		105.1
(-3)
P 		115.9
(-2.4)
P 		106
C 215.1
(3)
P 		196.8
(2.1)
P 		155.9
(0.1)
P 		94.9
(-2.9)
P 		121.8
(-1.6)
P 		93.1
(-3)
P 		122
avr 162.5
(0.8) 		196.2
(3) 		154.1
(0.3) 		127.6
(-1.4) 		108.2
(-2.6) 		102.4
(-3) 		94
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 56
1 2 3 4 range
A 73.9
(3)
P 		28.8
(-2.9)
P 		32.7
(-2.4)
P 		28.3
(-3)
P 		46
B 78.7
(3)
P 		31.9
(-2.5)
P 		28
(-3)
P 		34.5
(-2.2)
P 		51
C 82.7
(3)
P 		43.2
(-1.2)
P 		43.7
(-1.2)
P 		26.7
(-3)
P 		56
avr 78.4
(3) 		34.6
(-2.4) 		34.8
(-2.4) 		29.8
(-3) 		49

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 61
1 2 3 4 5 6 range
A 26.5
(-2.6)
P 		64.4
(3)
P 		27
(-2.5)
P 		36.7
(-1.1)
P 		29.4
(-2.2)
P 		23.9
(-3)
P 		41
B 44.7
(-1.7)
P 		70.1
(3)
P 		44.4
(-1.8)
P 		37.9
(-3)
P 		42.7
(-2.1)
P 		43.2
(-2)
P 		32
C 79.7
(3)
P 		60
(1)
P 		39.7
(-1)
P 		19.1
(-3)
P 		39.4
(-1)
P 		31.2
(-1.8)
P 		61
avr 50.3
(0.4) 		64.8
(3) 		37
(-2) 		31.2
(-3) 		37.2
(-1.9) 		32.8
(-2.7) 		34
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192317_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12871
Sequence Type Exemplar sequence
Representative Public ID F46F3.1 NCBI
Target Description F46F3.1 /REP_DB=WormBase Gene ID /WP=CE10586 /TR=Q9XVN4 /GB=CAB03112.1 /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_073551(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073551 NCBI Caenorhabditis elegans C.Elegans Homeobox family member (ceh-27) (ceh-27) mRNA, complete cds. 9/11 None
GENEFINDER00000004398 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11664365:11667286:-1 9/11 None
F46F3.1 ENSEMBL cdna:known chromosome:CEL140:V:11664259:11667286:-1 gene:F46F3.1 9/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000004389 7/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:11664371-11667286(-) 100.0 100.0
Public Domain and Genome References
Gene Title homeobox protein (NK-2 subfamily)
Gene Symbol ceh-27
Ensembl F46F3.1
Entrez Gene 185853 Entrez gene
SwissProt Q9XVN4 EMBL-EBI
WormBase CE36695 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 CAB03112 Hypothetical protein F46F3.1 [Caenorhabditis elegans] ref|NP_505952.3| C.Elegans Homeobox family member (ceh-27) [Caenorhabditis elegans] 1.0E-115
blast CAB03112 Hypothetical protein F46F3.1 [Caenorhabditis elegans] ref|NP_505952.3| C.Elegans Homeobox family member (ceh-27) [Caenorhabditis elegans] 1.0E-109
blast CAE75319 Hypothetical protein CBG23291 [Caenorhabditis briggsae] 3.0E-61
blast CAE75319 Hypothetical protein CBG23291 [Caenorhabditis briggsae] 4.0E-58
blast AAB49657 Nkx-related protein 2.0E-20
blast AAB49657 Nkx-related protein 3.0E-20
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999968265523E-22
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 8.00000025099516E-22
Pfam IPR001356 EMBL-EBI Homeobox 2.4E-27
Pfam IPR001356 EMBL-EBI Homeobox 2.4E-27
Sequence
Target Sequence 
>C. ELEGANS:192317_AT
attttaatcgcttccaaaccaatcagctgaatttgggacttacgacacagcagaatatga
tgatatcacgaagaaagcgacgtgttctcttctcacctcaacaagttcacgtcctggaac
gcaaattccaaatcaacagatatttgagcgccgcggatcgggaaaaccttgcgaagagta
ttaacttgtcggcaacacaggtgaaaatctggttccaaaatcaacgctacaagtgcaaga
gacaagaaaaagagaagaaaatggatggtggatgctatcgggatagtgacagggacactg
attcagacagagacaatgatagtagtggatcacttggaagttcgatgtctggaatcaaga
aggaagaagatgaagatcggaaaccattcatgccatcagcagtttcatctgatacagctt
gtcttccggatatctcacaacaagcattcccatatcaggttcgtattttagatttgttga
gactttcaaatcacaaaatcgtgttacaaataagattttgtgacgatgtacccttcgagt
tcatatatgcctccgttctt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTTTAATCGCTTCCAAACCAATCA 217 15 326 Antisense
GAATTTGGGACTTACGACACAGCAG 474 325 354 Antisense
AAGAAAGCGACGTGTTCTCTTCTCA 91 153 396 Antisense
ACCTCAACAAGTTCACGTCCTGGAA 259 85 420 Antisense
TGAGCGCCGCGGATCGGGAAAACCT 446 557 470 Antisense
GATCGGAAACCATTCATGCCATCAG 628 417 700 Antisense
ATCTGATACAGCTTGTCTTCCGGAT 708 33 732 Antisense
GATATCTCACAACAAGCATTCCCAT 127 427 754 Antisense
AGCATTCCCATATCAGGTTCGTATT 501 77 768 Antisense
TGTGACGATGTACCCTTCGAGTTCA 110 555 844 Antisense
CGAGTTCATATATGCCTCCGTTCTT 175 251 861 Antisense
Sequence Source Affymetrix Proprietary Database