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[191585_at] Homeobox domain

Description F58E6.10 /REP_DB=WormBase Gene ID /WP=CE06024 /GEN=unc-42 /TR=Q20455 /GB=CAA94780.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Homeobox domain
Cluster 6grp_total > 17      4grp_total > 23      6grp_cgc > 13      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 260
1 2 3 4 range
A 273.2
(3)
P 		122.4
(-2.2)
A 		100.6
(-3)
P 		196.8
(0.3)
P 		173
B 287.5
(2.9)
P 		118.3
(-2.1)
M 		86.4
(-3)
A 		291.2
(3)
P 		205
C 346.4
(3)
P 		115.5
(-2.5)
A 		94.9
(-3)
A 		219.9
(-0)
P 		252
avr 302.4
(3) 		118.7
(-2.3) 		94
(-3) 		236
(1.1) 		208

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 280
1 2 3 4 5 6 range
A 227.5
(3)
P 		209.3
(2.4)
P 		145.7
(0.2)
P 		115.2
(-0.8)
P 		50.9
(-3)
A 		126.6
(-0.4)
M 		177
B 307.8
(3)
P 		197.2
(-0.2)
P 		107.8
(-2.8)
P 		103.8
(-2.9)
A 		101.3
(-3)
A 		120.2
(-2.5)
P 		207
C 330.4
(3)
P 		165.9
(-1.4)
P 		139.1
(-2.1)
P 		104.6
(-3)
P 		108.4
(-2.9)
A 		123.6
(-2.5)
P 		226
avr 288.6
(3) 		190.8
(0.1) 		130.9
(-1.7) 		107.9
(-2.4) 		86.9
(-3) 		123.5
(-1.9) 		202
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 95
1 2 3 4 range
A 99.5
(3)
P 		26.6
(-3)
A 		26.3
(-3)
P 		28.8
(-2.8)
P 		73
B 91.7
(3)
P 		29.2
(-2.2)
M 		20
(-3)
A 		62.1
(0.5)
P 		72
C 114.7
(3)
P 		33.2
(-3)
A 		33.1
(-3)
A 		37.1
(-2.7)
P 		82
avr 102
(3) 		29.7
(-2.7) 		26.5
(-3) 		42.7
(-1.7) 		76

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 107
1 2 3 4 5 6 range
A 41.9
(-0.3)
P 		74.4
(3)
P 		31.7
(-1.3)
P 		29.2
(-1.6)
P 		15.4
(-3)
A 		30.8
(-1.4)
M 		59
B 107.1
(3)
P 		65.6
(-0.1)
P 		26.2
(-3)
P 		27.5
(-2.9)
A 		41.2
(-1.9)
A 		44.8
(-1.6)
P 		81
C 122.5
(3)
P 		50.6
(-1.3)
P 		35.4
(-2.1)
P 		21
(-3)
P 		35.1
(-2.2)
A 		41.4
(-1.8)
P 		102
avr 90.5
(3) 		63.5
(0.5) 		31.1
(-2.5) 		25.9
(-3) 		30.6
(-2.6) 		39
(-1.8) 		65
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191585_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12038
Sequence Type Exemplar sequence
Representative Public ID F58E6.10 NCBI
Target Description F58E6.10 /REP_DB=WormBase Gene ID /WP=CE06024 /GEN=unc-42 /TR=Q20455 /GB=CAA94780.1 /SUBMIT=HINXTON /CHR=5 /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_073118(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073118 NCBI Caenorhabditis elegans UNCoordinated family member (unc-42) (unc-42) mRNA, complete cds. 9/11 None
GENEFINDER00000040373 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9767228:9770931:-1 11/11 None
F58E6.10 ENSEMBL cdna:known chromosome:CEL140:V:9767228:9771851:-1 gene:F58E6.10 9/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000040370 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:9767227-9771851(-) 100.0 100.0
Public Domain and Genome References
Gene Title Homeobox domain
Gene Symbol unc-42
Ensembl F58E6.10
Entrez Gene 192081 Entrez gene
SwissProt Q20455 EMBL-EBI
WormBase CE36596 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 NP_505519 UNCoordinated family member (unc-42) [Caenorhabditis elegans] 1.0E-142
blast CAA94830 Hypothetical protein F58E6.10 [Caenorhabditis elegans] emb|CAA94780.3| Hypothetical protein F58E6.10 [Caenorhabditis elegans] 1.0E-129
blast CAE72250 Hypothetical protein CBG19368 [Caenorhabditis briggsae] 1.0E-109
blast NP_505519 UNCoordinated family member (unc-42) [Caenorhabditis elegans] 1.0E-104
blast CAA94830 Hypothetical protein F58E6.10 [Caenorhabditis elegans] emb|CAA94780.3| Hypothetical protein F58E6.10 [Caenorhabditis elegans] 1.0E-103
blast CAE72250 Hypothetical protein CBG19368 [Caenorhabditis briggsae] 5.0E-92
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 3.00000003404354E-18
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 2.00000003908296E-24
Pfam IPR001356 EMBL-EBI Homeobox 4.0E-30
Pfam IPR001356 EMBL-EBI Homeobox 3.2E-20
Sequence
Target Sequence 
>C. ELEGANS:191585_AT
gatgttgcagatggcgccttcaaaaagattaaaaccgaagactcggtggctcggtatttg
gatcttcgattgctggggtcacgaacacgcctgcaaggagcttgatgctgcattccaaaa
gagtcactatccggatatctacgttcgagaggaattggcaaggatcaccaagttgaatga
agctcgaatacaggtgtggttccaaaatcggcgagcaaaacatcggaagcatgaaaaaca
attgaataaggcaatcaatcccccgcactcattcctatccaatccagcgaatactttgat
gcgacaaggaatgtacccagctgcattgaatcgtgacggtttttggtatcaatcatatca
acgaccaatgccatacccaacagcttctccttcatattccaactcgttcactaatcccat
tgcaaatttcggtcattccatcacctctttccaagctgacgacgagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGTTGCAGATGGCGCCTTCAAAA 145 411 192 Antisense
GACTCGGTGGCTCGGTATTTGGATC 94 373 231 Antisense
TGGATCTTCGATTGCTGGGGTCACG 144 551 250 Antisense
GTCACGAACACGCCTGCAAGGAGCT 18 467 269 Antisense
CACTATCCGGATATCTACGTTCGAG 307 195 316 Antisense
TGAATAAGGCAATCAATCCCCCGCA 656 571 434 Antisense
GTACCCAGCTGCATTGAATCGTGAC 294 459 504 Antisense
TATCAACGACCAATGCCATACCCAA 476 657 547 Antisense
CTCGTTCACTAATCCCATTGCAAAT 632 231 594 Antisense
GCAAATTTCGGTCATTCCATCACCT 314 317 613 Antisense
ACCTCTTTCCAAGCTGACGACGAGT 81 89 634 Antisense
Sequence Source Affymetrix Proprietary Database