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[192928_at] so class homeobox protein

Description F56A12.1 /REP_DB=WormBase Gene ID /WP=CE11222 /GEN=ceh-35 /TR=O17894 /GB=CAB04483.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=so class homeobox protein
Cluster 6grp_total > 36      4grp_total > 47      6grp_cgc > 15      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 134
1 2 3 4 range
A 115.5
(3)
P 		56.9
(-2.4)
A 		94.3
(1.1)
A 		50
(-3)
A 		66
B 160.6
(3)
A 		103
(-0.9)
A 		72.2
(-3)
A 		77.8
(-2.6)
A 		88
C 184.1
(3)
A 		85.1
(-2.1)
A 		66.6
(-3)
A 		91.7
(-1.7)
P 		118
avr 153.4
(3) 		81.7
(-2.4) 		77.7
(-2.7) 		73.2
(-3) 		80

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 147
1 2 3 4 5 6 range
A 180.6
(3)
P 		75.8
(-1.3)
A 		77
(-1.2)
A 		36.9
(-2.9)
A 		33.4
(-3)
A 		140.5
(1.4)
M 		147
B 154.4
(3)
P 		153.9
(3)
P 		74.8
(-1.3)
A 		43.6
(-3)
A 		71.3
(-1.5)
A 		76.2
(-1.2)
P 		111
C 77.9
(-0.3)
A 		121.6
(3)
A 		66.5
(-1.2)
A 		86.1
(0.3)
A 		42.5
(-3)
A 		81.5
(-0)
M 		79
avr 137.6
(3) 		117.1
(1.6) 		72.8
(-1.4) 		55.5
(-2.6) 		49.1
(-3) 		99.4
(0.4) 		89
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 54
1 2 3 4 range
A 42.1
(3)
P 		12.4
(-2.1)
A 		24.7
(-0)
A 		7.3
(-3)
A 		35
B 51.2
(3)
A 		25.4
(-1.5)
A 		16.7
(-3)
A 		16.6
(-3)
A 		35
C 60.9
(3)
A 		24.5
(-1.8)
A 		23.2
(-2)
A 		15.5
(-3)
P 		45
avr 51.4
(3) 		20.8
(-1.8) 		21.5
(-1.7) 		13.1
(-3) 		38

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 44
1 2 3 4 5 6 range
A 33.3
(2.8)
P 		26.9
(1.2)
A 		16.8
(-1.2)
A 		9.4
(-3)
A 		10.1
(-2.8)
A 		34.2
(3)
M 		25
B 53.7
(3)
P 		51.2
(2.6)
P 		18.2
(-2.1)
A 		11.6
(-3)
A 		29
(-0.5)
A 		28.4
(-0.6)
P 		42
C 28.9
(0.9)
A 		37.1
(3)
A 		16.9
(-2.2)
A 		17.3
(-2.1)
A 		13.8
(-3)
A 		27.3
(0.5)
M 		23
avr 38.6
(3) 		38.4
(3) 		17.3
(-2) 		12.8
(-3) 		17.6
(-1.9) 		30
(1) 		26
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192928_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12882
Sequence Type Exemplar sequence
Representative Public ID F56A12.1 NCBI
Target Description F56A12.1 /REP_DB=WormBase Gene ID /WP=CE11222 /GEN=ceh-35 /TR=O17894 /GB=CAB04483.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=so class homeobox protein
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_074162(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074162 NCBI Caenorhabditis elegans UNCoordinated family member (unc-39) (unc-39) mRNA, complete cds. 11/11 None
F56A12.1 ENSEMBL cdna:known chromosome:CEL140:V:14375977:14378387:1 gene:F56A12.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000028034 4/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:14375976-14378387(+) 100.0 100.0
Public Domain and Genome References
Gene Title so class homeobox protein
Gene Symbol unc-39
Ensembl F56A12.1
Entrez Gene 191623 Entrez gene
SwissProt O17894 EMBL-EBI
WormBase CE37921 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 CAB04483 Hypothetical protein F56A12.1 [Caenorhabditis elegans] ref|NP_506563.2| UNCoordinated family member (unc-39) [Caenorhabditis elegans] 1.0E-157
blast CAE60911 Hypothetical protein CBG04628 [Caenorhabditis briggsae] 3.0E-92
blast CAF97439 unnamed protein product [Tetraodon nigroviridis] 5.0E-37
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 8.00000009348878E-7
Pfam IPR001356 EMBL-EBI Homeobox 1.5E-6
Sequence
Target Sequence 
>C. ELEGANS:192928_AT
atcgtagcctacacatatgccttatatcattccaatgaattcgagacactcttccacctt
ctctcgaatcgacattttcaacagcgtcattacaatgatctacaagatatttggcatcat
gcaaggtacaaggaaagtcagctgaaacgtggcaaagaactgaatccagtggaaaaatat
cggctgagacgaaagtttccggctccgaaaacaatttgggatggtgaggagattgtgtac
agtttcaaggattcgagtaggaaatttttgaaacaatttttccgcaacgtctctgaatat
ccgacccaggagcagaaaagagagatttcaagagcaacaggactcaaaattgtacaggtt
tgtgagaaaaatattaacttcaaaattgcttatttaatttcaaattggttcaaaaaccgt
cgccaacgggacaaatcgaacaattcagccaaatgctccccaccttccagctcgagcagc
actaatggtggcagtgactttcttccaataataactccgcaaagctttaacttggcagct
gctccattcaat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATCGTAGCCTACACATATGCCTTAT 523 35 439 Antisense
ATGAATTCGAGACACTCTTCCACCT 197 43 473 Antisense
CCACCTTCTCTCGAATCGACATTTT 31 275 492 Antisense
AAACAATTTTTCCGCAACGTCTCTG 40 129 709 Antisense
GTCTCTGAATATCCGACCCAGGAGC 183 471 727 Antisense
GAACAATTCAGCCAAATGCTCCCCA 178 353 876 Antisense
TTCCAGCTCGAGCAGCACTAATGGT 133 695 903 Antisense
ATGGTGGCAGTGACTTTCTTCCAAT 669 49 923 Antisense
GACTTTCTTCCAATAATAACTCCGC 677 369 934 Antisense
AACTCCGCAAAGCTTTAACTTGGCA 224 141 951 Antisense
TAACTTGGCAGCTGCTCCATTCAAT 266 637 966 Antisense
Sequence Source Affymetrix Proprietary Database