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[189007_at] homeobox protein

Description M6.3 /REP_DB=WormBase Gene ID /WP=CE07384 /TR=Q21578 /GB=AAA98706.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=homeobox protein
Cluster 6grp_total > 60      4grp_total > 01      6grp_cgc > 94      6grp_cgc_sub > 04      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 37
1 2 3 4 range
A 3.3
(-3)
A 		5.8
(-1.7)
A 		6
(-1.6)
A 		15.2
(3)
A 		12
B 9.5
(-2.5)
A 		6.6
(-3)
A 		13.7
(-1.7)
A 		40.3
(3)
A 		34
C 9.6
(-0.8)
A 		6.9
(-2.4)
A 		5.8
(-3)
A 		16.4
(3)
A 		11
avr 7.5
(-2.6) 		6.4
(-3) 		8.5
(-2.3) 		24
(3) 		18

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 18
1 2 3 4 5 6 range
A 6.7
(-1)
A 		7.2
(-0.7)
A 		13.1
(3)
A 		6.4
(-1.2)
A 		3.5
(-3)
A 		6.5
(-1.1)
A 		10
B 9
(2.7)
A 		5.1
(-1.1)
A 		8.3
(2)
A 		9.3
(3)
A 		3.2
(-3)
A 		4.4
(-1.8)
A 		6
C 8.8
(-1.9)
A 		6.7
(-2.8)
A 		7.1
(-2.6)
A 		21.1
(3)
A 		6.1
(-3)
A 		12.9
(-0.3)
A 		15
avr 8.2
(-0.1) 		6.3
(-1.5) 		9.5
(0.9) 		12.3
(3) 		4.3
(-3) 		7.9
(-0.3) 		8
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7
1 2 3 4 range
A 1.2
(-3)
A 		1.3
(-2.4)
A 		1.6
(-0.6)
A 		2.2
(3)
A 		1
B 3
(-1.8)
A 		1.6
(-3)
A 		3.2
(-1.6)
A 		8.6
(3)
A 		7
C 3.2
(3)
A 		2
(-3)
A 		2
(-3)
A 		2.8
(1)
A 		1
avr 2.5
(-1.1) 		1.6
(-3) 		2.3
(-1.6) 		4.5
(3) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3
1 2 3 4 5 6 range
A 1.2
(-2.7)
A 		2.6
(2)
A 		2.9
(3)
A 		1.6
(-1.3)
A 		1.1
(-3)
A 		1.6
(-1.3)
A 		2
B 3.1
(3)
A 		1.7
(-1.7)
A 		2
(-0.7)
A 		2.5
(1)
A 		1.3
(-3)
A 		1.6
(-2)
A 		2
C 3.3
(0.6)
A 		2.1
(-2.3)
A 		1.8
(-3)
A 		4.2
(2.8)
A 		2
(-2.5)
A 		4.3
(3)
A 		3
avr 2.5
(1.6) 		2.1
(-0.2) 		2.2
(0.2) 		2.8
(3) 		1.5
(-3) 		2.5
(1.6) 		1
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189007_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18554
Sequence Type Exemplar sequence
Representative Public ID M6.3 NCBI
Target Description M6.3 /REP_DB=WormBase Gene ID /WP=CE07384 /TR=Q21578 /GB=AAA98706.1 /SUBMIT=ST.LOUIS /CHR=X /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_075730(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075730 NCBI Caenorhabditis elegans defective PHArynx development family member (pha-2) (pha-2) mRNA, complete cds. 9/11 None
GENEFINDER00000028058 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:633718:636879:-1 9/11 None
SNAP00000028055 ENSEMBL cdna:SNAP chromosome:CEL140:X:634755:636622:-1 9/11 None
M6.3 ENSEMBL cdna:known chromosome:CEL140:X:633702:637042:-1 gene:M6.3 9/11 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
chrX:633717-637042(-) 100.0 100.0
Public Domain and Genome References
Gene Title homeobox protein
Gene Symbol pha-2
Ensembl M6.3
Entrez Gene 187454 Entrez gene
SwissProt Q21578 EMBL-EBI
WormBase CE37784 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 AAA98706 Defective pharynx development protein 2 [Caenorhabditis elegans] ref|NP_508131.2| defective PHArynx development family member (pha-2) [Caenorhabditis elegans] 1.0E-120
blast AAA98706 Defective pharynx development protein 2 [Caenorhabditis elegans] ref|NP_508131.2| defective PHArynx development family member (pha-2) [Caenorhabditis elegans] 2.0E-99
blast AAV34757 PHA-2 [Caenorhabditis elegans] 1.0E-97
blast AAV34757 PHA-2 [Caenorhabditis elegans] 2.0E-97
blast CAE63640 Hypothetical protein CBG08137 [Caenorhabditis briggsae] 1.0E-74
blast CAE63640 Hypothetical protein CBG08137 [Caenorhabditis briggsae] 4.0E-69
blast AAV34757 PHA-2 [Caenorhabditis elegans] 8.0E-58
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 5.99999978589949E-8
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999983775159E-18
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 2.00000009162741E-18
Pfam IPR001356 EMBL-EBI Homeobox 4.1E-27
Pfam IPR001356 EMBL-EBI Homeobox 4.1E-27
Pfam IPR001356 EMBL-EBI Homeobox 4.0E-10
Sequence
Target Sequence 
>C. ELEGANS:189007_AT
gaactctcgactttaatccgtggatatgtcatgttagccagcaactagcagcacagctat
cacagaacggtaaaaatcgacctggtgctccaaatcaagttccgcttctgaacatgaatg
tcaatcagacgatgggaaatatgtgggatcctcggctttcatggttgtacccgtacatga
gcaagtccccgcagaagaggaaaggaggacagataaggttcattttctattataatcttg
ctcgaaacgacatttcaaattataaatgtcacgtctcctttcgatgttctcataacgata
ctatacgattcagattcaccaatgagcaaaccgatgcgttggagcacaaattcgattcac
ataagtatttgagtccccaagagcggaagaaacttgcaaagtctttgagcctcagcgagc
gacaggttaaaacatggtttcaaaacagaagggcaaaatggcgtcgtgtacgtaaggatg
gtgaggatgaggatgaaatgcctaatggagcgtcagcaagaagcctcggacagc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAACTCTCGACTTTAATCCGTGGAT 320 349 218 Antisense
GTTAGCCAGCAACTAGCAGCACAGC 436 447 250 Antisense
GCAGCACAGCTATCACAGAACGGTA 188 313 265 Antisense
AAAATCGACCTGGTGCTCCAAATCA 220 133 290 Antisense
CTCCAAATCAAGTTCCGCTTCTGAA 694 233 305 Antisense
TCCTCGGCTTTCATGGTTGTACCCG 22 589 366 Antisense
TTGTACCCGTACATGAGCAAGTCCC 533 657 382 Antisense
TATAAATGTCACGTCTCCTTTCGAT 650 659 478 Antisense
GTCTCCTTTCGATGTTCTCATAACG 227 471 490 Antisense
TTGAGCCTCAGCGAGCGACAGGTTA 466 705 622 Antisense
GCGTCAGCAAGAAGCCTCGGACAGC 554 291 727 Antisense
Sequence Source Affymetrix Proprietary Database