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[189632_at] homeobox protein

Description C09G12.1 /REP_DB=WormBase Gene ID /WP=CE16835 /TR=O44462 /GB=AAC25819.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=homeobox protein
Cluster 6grp_total > 45      4grp_total > 44      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 41
1 2 3 4 range
A 13.9
(-2.3)
A 		40
(3)
A 		10.6
(-3)
A 		14.9
(-2.1)
A 		29
B 50.2
(3)
A 		36.2
(1)
A 		14
(-2.3)
A 		9
(-3)
A 		41
C 14.2
(3)
A 		13.9
(2.6)
A 		9.8
(-3)
A 		12.1
(0.1)
A 		4
avr 26.1
(1.7) 		30
(3) 		11.5
(-3) 		12
(-2.8) 		19

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 20
1 2 3 4 5 6 range
A 16.9
(1.2)
A 		3
(-3)
A 		22.7
(3)
A 		5.8
(-2.1)
A 		7.9
(-1.5)
A 		18.3
(1.7)
A 		20
B 7.1
(-2)
A 		10.5
(3)
A 		6.4
(-3)
A 		9.2
(1.1)
A 		7.1
(-2)
A 		8.4
(-0.1)
A 		4
C 8.1
(-0.5)
A 		12.3
(3)
A 		5.1
(-3)
A 		8.3
(-0.3)
A 		7.1
(-1.3)
A 		5.9
(-2.3)
A 		7
avr 10.7
(2) 		8.6
(-1.2) 		11.4
(3) 		7.8
(-2.4) 		7.4
(-3) 		10.9
(2.3) 		4
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14
1 2 3 4 range
A 5
(-0.4)
A 		8.7
(3)
A 		2.8
(-2.4)
A 		2.2
(-3)
A 		7
B 16
(3)
A 		8.9
(-0)
A 		3.2
(-2.4)
A 		1.9
(-3)
A 		14
C 4.7
(3)
A 		4
(1.4)
A 		3.4
(0.1)
A 		2
(-3)
A 		3
avr 8.6
(3) 		7.2
(1.7) 		3.1
(-2) 		2
(-3) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4
1 2 3 4 5 6 range
A 3.1
(0.2)
A 		1.1
(-3)
A 		4.9
(3)
A 		1.5
(-2.4)
A 		2.4
(-0.9)
A 		4.5
(2.4)
A 		4
B 2.5
(-0.2)
A 		3.5
(3)
A 		1.6
(-3)
A 		2.4
(-0.5)
A 		2.9
(1.1)
A 		3.1
(1.7)
A 		2
C 3
(1.3)
A 		3.7
(3)
A 		1.3
(-3)
A 		1.7
(-2)
A 		2.3
(-0.5)
A 		2
(-1.3)
A 		2
avr 2.9
(1.6) 		2.8
(1.2) 		2.6
(0.2) 		1.9
(-3) 		2.5
(-0.2) 		3.2
(3) 		1
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189632_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11084
Sequence Type Exemplar sequence
Representative Public ID C09G12.1 NCBI
Target Description C09G12.1 /REP_DB=WormBase Gene ID /WP=CE16835 /TR=O44462 /GB=AAC25819.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=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_067960(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067960 NCBI Caenorhabditis elegans C09G12.1 (C09G12.1) mRNA, complete cds. 11/11 None
SNAP00000001979 ENSEMBL cdna:SNAP chromosome:CEL140:IV:3498292:3503840:1 9/11 None
GENEFINDER00000001990 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:3502136:3506276:1 9/11 None
C09G12.1 ENSEMBL cdna:known chromosome:CEL140:IV:3501650:3503457:1 gene:C09G12.1 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
chrIV:3501658-3503463(+) 72.7 99.61
Public Domain and Genome References
Gene Title homeobox protein
Ensembl C09G12.1
Entrez Gene 182467 Entrez gene
SwissProt O44462 EMBL-EBI
WormBase CE16835 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 AAT92087 Serpentine receptor, class z protein 83 [Caenorhabditis elegans] ref|NP_001021314.1| Serpentine Receptor, class Z family member (srz-83) [Caenorhabditis elegans] 1.0E-100
blast AAC25819 Hypothetical protein C09G12.1 [Caenorhabditis elegans] ref|NP_500361.1| C09G12.1 [Caenorhabditis elegans] 4.0E-96
blast AAC25819 Hypothetical protein C09G12.1 [Caenorhabditis elegans] ref|NP_500361.1| C09G12.1 [Caenorhabditis elegans] 8.0E-59
blast AAC25819 Hypothetical protein C09G12.1 [Caenorhabditis elegans] ref|NP_500361.1| C09G12.1 [Caenorhabditis elegans] 2.0E-58
blast AAZ42339 putative homeobox protein [Caenorhabditis remanei] 3.0E-38
blast AAT92088 Serpentine receptor, class z protein 82 [Caenorhabditis elegans] ref|NP_001021315.1| Serpentine Receptor, class Z family member (srz-82) [Caenorhabditis elegans] 1.0E-37
blast AAZ42339 putative homeobox protein [Caenorhabditis remanei] 2.0E-36
blast CAE69034 Hypothetical protein CBG15039 [Caenorhabditis briggsae] 3.0E-36
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 3.0000001167616E-16
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 1.99999996755032E-17
Pfam IPR001356 EMBL-EBI Homeobox 2.4E-26
Pfam IPR001356 EMBL-EBI Homeobox 2.4E-26
Pfam IPR003845 EMBL-EBI Protein of unknown function DUF216 4.5E-18
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000001990 6 243-262,266-285,302-319,334-356,376-398,408-430
Sequence
Target Sequence 
>C. ELEGANS:189632_AT
ggtcattccctagtcagtttatgccaatgctcttcctcgccaccacaatcagctcaaaat
tccgaggaacgtcgcgtacgtcggctccggacagctttctctgaaaatcagctggaattg
ttggaagaagcttttctgaaatgtcagtatccggatgttcagcagcgagagaccctgggg
aagcaaacagagctcgccgaggcccgaattcaggtttggttcaaaaatcgcagagcaaaa
gcccgtaaacgacagcgaaacgagagtaccgatagctgcagtactactgaagaatccaat
gaggaaggcgatgcagatgggtgtttgaagaaaaaagcaaagaatgaaacgacaattatt
acctggacacccggagcagctctattcaactcgtcgctgagccccaccaccacatcgatt
ccgacaactccggctccgccactgaactttatctgtcatcagaatccgttttatgcatac
aacccg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGTCATTCCCTAGTCAGTTTATGCC 323 503 208 Antisense
TCAGTTTATGCCAATGCTCTTCCTC 601 623 221 Antisense
TCCGAGGAACGTCGCGTACGTCGGC 260 589 268 Antisense
GCTCCGGACAGCTTTCTCTGAAAAT 347 299 291 Antisense
GTCAGTATCCGGATGTTCAGCAGCG 309 467 350 Antisense
TTCAGCAGCGAGAGACCCTGGGGAA 644 687 365 Antisense
GGGAAGCAAACAGAGCTCGCCGAGG 509 493 385 Antisense
CAATTATTACCTGGACACCCGGAGC 503 177 560 Antisense
GCAGCTCTATTCAACTCGTCGCTGA 471 313 583 Antisense
TCCGCCACTGAACTTTATCTGTCAT 151 597 642 Antisense
GAATCCGTTTTATGCATACAACCCG 429 327 669 Antisense
Sequence Source Affymetrix Proprietary Database