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[192022_at] Homeobox domain

Description F17A2.5 /REP_DB=WormBase Gene ID /WP=CE03215 /GEN=ceh-40 /TR=SW:Q19503 /GB=CAA92154.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=Homeobox domain
Cluster 6grp_total > 87      4grp_total > 09      6grp_cgc > 58      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 79
1 2 3 4 range
A 10.7
(-2.8)
A 		8.7
(-3)
A 		36.7
(-0.8)
A 		86.4
(3)
A 		78
B 12.5
(-1.9)
A 		8.8
(-2.7)
A 		7.1
(-3)
A 		37.6
(3)
A 		31
C 10.7
(-3)
A 		21.8
(-1.7)
A 		17.5
(-2.2)
A 		61.1
(3)
A 		50
avr 11.3
(-3) 		13.1
(-2.8) 		20.4
(-1.9) 		61.7
(3) 		50

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 115
1 2 3 4 5 6 range
A 12.4
(-2.6)
A 		41.5
(-1.1)
A 		5.6
(-3)
A 		29.4
(-1.8)
A 		31.4
(-1.7)
A 		120.3
(3)
A 		115
B 7.2
(-2.9)
A 		5.9
(-3)
A 		7.6
(-2.9)
A 		59.9
(-0.2)
A 		73.5
(0.6)
A 		120
(3)
P 		114
C 9.1
(-3)
A 		38
(-1.2)
A 		39.6
(-1.1)
A 		28.3
(-1.8)
A 		78.6
(1.4)
A 		103.8
(3)
P 		95
avr 9.6
(-3) 		28.5
(-1.9) 		17.6
(-2.5) 		39.2
(-1.3) 		61.2
(-0.1) 		114.7
(3) 		105
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 11
1 2 3 4 range
A 3.9
(-1.9)
A 		1.9
(-3)
A 		9.6
(1.3)
A 		12.6
(3)
A 		11
B 4
(-0.8)
A 		2.2
(-2.4)
A 		1.6
(-3)
A 		8
(3)
A 		6
C 3.5
(-3)
A 		6.3
(-0.5)
A 		6.1
(-0.7)
A 		10.3
(3)
A 		7
avr 3.8
(-2.7) 		3.5
(-3) 		5.8
(-1) 		10.3
(3) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 44
1 2 3 4 5 6 range
A 2.3
(-2.8)
A 		14.7
(-0.1)
A 		1.2
(-3)
A 		7.5
(-1.7)
A 		9.5
(-1.2)
A 		29.3
(3)
A 		28
B 2.5
(-2.9)
A 		2
(-3)
A 		1.9
(-3)
A 		15.9
(-1)
A 		29.9
(0.9)
A 		44.8
(3)
P 		43
C 3.4
(-3)
A 		11.6
(-1.4)
A 		10.1
(-1.7)
A 		5.7
(-2.6)
A 		25.4
(1.2)
A 		34.7
(3)
P 		31
avr 2.7
(-3) 		9.4
(-1.8) 		4.4
(-2.7) 		9.7
(-1.8) 		21.6
(0.4) 		36.3
(3) 		34
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192022_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16118
Sequence Type Exemplar sequence
Representative Public ID F17A2.5 NCBI
Target Description F17A2.5 /REP_DB=WormBase Gene ID /WP=CE03215 /GEN=ceh-40 /TR=SW:Q19503 /GB=CAA92154.1 /SUBMIT=HINXTON /CHR=X /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_077659(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077659 NCBI Caenorhabditis elegans C.Elegans Homeobox family member (ceh-40) (ceh-40) mRNA, complete cds. 11/11 None
SNAP00000014130 ENSEMBL cdna:SNAP chromosome:CEL140:X:12318161:12320621:-1 11/11 None
GENEFINDER00000014137 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:12318161:12320621:-1 11/11 None
F17A2.5 ENSEMBL cdna:known chromosome:CEL140:X:12318161:12320621:-1 gene:F17A2.5 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
chrX:12318160-12320621(-) 100.0 100.0
Public Domain and Genome References
Gene Title Homeobox domain
Gene Symbol ceh-40
Ensembl F17A2.5
Entrez Gene 191624 Entrez gene
SwissProt Q19503 EMBL-EBI
WormBase CE03215 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 CAA92154 Hypothetical protein F17A2.5 [Caenorhabditis elegans] ref|NP_510060.1| C.Elegans Homeobox family member (ceh-40) [Caenorhabditis elegans] sp|Q19503|HM40_CAEEL Homeobox protein ceh-40 0.0
blast CAE70060 Hypothetical protein CBG16494 [Caenorhabditis briggsae] 3.0E-67
blast AAA81691 C.elegans homeobox protein 20 [Caenorhabditis elegans] ref|NP_001022555.1| C.Elegans Homeobox family member (ceh-20) [Caenorhabditis elegans] sp|P41779|HM20_CAEEL Homeobox protein ceh-20 gb|AAC46471.1| Ceh-20 3.0E-67
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 1.00000001954148E-25
Pfam IPR001356 EMBL-EBI Homeobox 1.8E-15
Pfam IPR005542 EMBL-EBI PBX domain 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:192022_AT
caaggagaattccgtccaatcacccaacagtcaaccgaaaagtttatgaacaagatgtcc
ggtaaatttaacaaggtctgttttgtactaaaacagactgcctgcgaagaagttatccaa
ctgaaaaagcgttatctggatgctcgtcgaaagagaagaaatttctcgaaaacttccacc
gagattctcaacgagtacttcctagcaaacatcaatcatccatacccgtcggaagaggtc
aaacaggccttagctatgcaatgtaacattagtgttgctcaggtatcaaactggtttgga
aataagcgaattcgctacaagaaaacaatggctaagaatgaggatgaaagaagagaaaac
agaaaaccagaagatcgccctccgcctggagctcctggagctccgtatagtctggtaccc
aacgcgtttgcaggaatgatgaacccatatcagatgatgttacctggtcatcaatttccc
atcggtgttgcccctttcaatttttccatgtacaatcctgag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAAGGAGAATTCCGTCCAATCACCC 351 183 430 Antisense
AATCACCCAACAGTCAACCGAAAAG 580 169 447 Antisense
GACTGCCTGCGAAGAAGTTATCCAA 321 375 525 Antisense
GCGTTATCTGGATGCTCGTCGAAAG 684 289 558 Antisense
GAGTACTTCCTAGCAAACATCAATC 491 397 622 Antisense
TCAATCATCCATACCCGTCGGAAGA 390 633 641 Antisense
GGTCAAACAGGCCTTAGCTATGCAA 622 501 666 Antisense
TCCTGGAGCTCCGTATAGTCTGGTA 493 591 822 Antisense
GTACCCAACGCGTTTGCAGGAATGA 11 459 844 Antisense
GTTACCTGGTCATCAATTTCCCATC 279 447 888 Antisense
CAATTTTTCCATGTACAATCCTGAG 420 179 927 Antisense
Sequence Source Affymetrix Proprietary Database