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[194012_s_at]

Description F14F3.1 /REP_DB=WormBase Gene ID /WP=CE24899 /CHR=X /FEA=Sanger Annotation /DEF=locus:vab-3 Paired box domain, homeobox protein (paired subfamily) (HINXTON) TR:Q17359 protein_id:CAA90186.2
Cluster 6grp_high1_10_10 > 14      4grp_highest_8_8 > 56      4grp_high_8_8 > 35      6grp_total > 03      4grp_total > 45      6grp_cgc > 42      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 230
1 2 3 4 range
A 339
(3)
P 		131.3
(-3)
P 		175
(-1.7)
P 		149.9
(-2.5)
P 		208
B 253.7
(0)
P 		361.3
(3)
P 		143.5
(-3)
P 		190.9
(-1.7)
P 		218
C 279.1
(3)
P 		279.5
(3)
P 		220.4
(0.4)
P 		144.6
(-3)
P 		135
avr 290.6
(3) 		257.4
(1.5) 		179.6
(-2.2) 		161.8
(-3) 		129

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 166
1 2 3 4 5 6 range
A 227.9
(3)
P 		197.3
(1.5)
P 		178
(0.5)
P 		161.2
(-0.3)
P 		144.7
(-1.2)
A 		108.3
(-3)
P 		120
B 245.1
(3)
P 		213.1
(1.8)
P 		133.9
(-1.1)
P 		150.6
(-0.5)
P 		232.5
(2.5)
P 		81.9
(-3)
P 		163
C 199.3
(1.2)
P 		247.5
(3)
P 		223.4
(2.1)
P 		161.2
(-0.1)
P 		136.5
(-1)
P 		82.3
(-3)
P 		165
avr 224.1
(3) 		219.3
(2.8) 		178.4
(0.9) 		157.7
(0) 		171.2
(0.6) 		90.8
(-3) 		133
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 102
1 2 3 4 range
A 123.4
(3)
P 		28.5
(-2.6)
P 		45.7
(-1.6)
P 		21.9
(-3)
P 		102
B 80.9
(2.1)
P 		89.2
(3)
P 		33.3
(-3)
P 		40.7
(-2.2)
P 		56
C 92.4
(3)
P 		80.3
(1.9)
P 		76.8
(1.6)
P 		24.4
(-3)
P 		68
avr 98.9
(3) 		66
(0.2) 		51.9
(-1) 		29
(-3) 		70

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 68
1 2 3 4 5 6 range
A 42
(-0.9)
P 		70.2
(3)
P 		38.8
(-1.3)
P 		40.9
(-1)
P 		43.7
(-0.6)
A 		26.4
(-3)
P 		44
B 85.3
(2.1)
P 		70.9
(0.8)
P 		32.5
(-2.8)
P 		39.9
(-2.1)
P 		94.4
(3)
P 		30.6
(-3)
P 		64
C 73.9
(2.8)
P 		75.5
(3)
P 		56.9
(0.7)
P 		32.4
(-2.4)
P 		44.2
(-0.9)
P 		27.6
(-3)
P 		48
avr 67.1
(2.3) 		72.2
(3) 		42.7
(-1) 		37.7
(-1.7) 		60.8
(1.4) 		28.2
(-3) 		44
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194012_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16032
Sequence Type Exemplar sequence
Representative Public ID F14F3.1 NCBI
Target Description F14F3.1 /REP_DB=WormBase Gene ID /WP=CE24899 /CHR=X /FEA=Sanger Annotation /DEF=locus:vab-3 Paired box domain, homeobox protein (paired subfamily) (HINXTON) TR:Q17359 protein_id:CAA90186.2
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,GenBank identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_001029399(11), NM_001029400(11), NM_001029401(11), U29145(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001029399 NCBI Caenorhabditis elegans Variable ABnormal morphology family member (vab-3) (vab-3) mRNA, complete cds. 11/11 None
NM_001029400 NCBI Caenorhabditis elegans Variable ABnormal morphology family member (vab-3) (vab-3) mRNA, complete cds. 11/11 None
NM_001029401 NCBI Caenorhabditis elegans Variable ABnormal morphology family member (vab-3) (vab-3) mRNA, complete cds. 11/11 None
U29145 NCBI Caenorhabditis elegans (mab-18) mRNA, transcript #1, complete cds. 11/11 None
GENEFINDER00000003729 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:10505878:10518577:1 11/11 None
F14F3.1a ENSEMBL cdna:known chromosome:CEL140:X:10499862:10519502:1 gene:F14F3.1 11/11 A 
F14F3.1b ENSEMBL cdna:known chromosome:CEL140:X:10515350:10518577:1 gene:F14F3.1 11/11 None
F14F3.1c ENSEMBL cdna:known chromosome:CEL140:X:10515914:10519502:1 gene:F14F3.1 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000003723 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:10509376-10518577(+) 99.63 99.63
Public Domain and Genome References
Ensembl F14F3.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA90186 Hypothetical protein F14F3.1a [Caenorhabditis elegans] ref|NP_001024570.1| Variable ABnormal morphology family member (vab-3) [Caenorhabditis elegans] gb|AAA82991.1| variable abnormal-3 prf||2120399A vab-3 gene 0.0
blast CAC42288 Hypothetical protein F14F3.1c [Caenorhabditis elegans] ref|NP_001024572.1| Variable ABnormal morphology family member (vab-3) [Caenorhabditis elegans] gb|AAC47542.1| MAB-18 prf||2120400B mab-18 gene 1.0E-160
blast AAC47541 MAB-18 prf||2120400A mab-18 gene 1.0E-154
blast CAC42287 Hypothetical protein F14F3.1b [Caenorhabditis elegans] ref|NP_001024571.1| Variable ABnormal morphology family member (vab-3) [Caenorhabditis elegans] 1.0E-144
blast AAC47541 MAB-18 prf||2120400A mab-18 gene 1.0E-141
blast CAA90186 Hypothetical protein F14F3.1a [Caenorhabditis elegans] ref|NP_001024570.1| Variable ABnormal morphology family member (vab-3) [Caenorhabditis elegans] gb|AAA82991.1| variable abnormal-3 prf||2120399A vab-3 gene 1.0E-141
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 2.99999996001683E-24
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 2.00000003908296E-24
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 3.00000005862444E-25
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 2.00000003908296E-25
scop a.4.1.Paired domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Paired domain 3.0000000817356E-27
scop a.4.1.Paired domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Paired domain 4.0000001089808E-27
scop a.4.1.Paired domain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Paired domain 4.00000007816593E-25
Pfam IPR001523 EMBL-EBI Paired box protein, N-terminal 1.7E-81
Pfam IPR001356 EMBL-EBI Homeobox 4.2E-29
Pfam IPR001356 EMBL-EBI Homeobox 4.2E-29
Pfam IPR001356 EMBL-EBI Homeobox 4.2E-29
Pfam IPR001356 EMBL-EBI Homeobox 4.2E-29
Pfam IPR001523 EMBL-EBI Paired box protein, N-terminal 1.7E-81
Pfam IPR001356 EMBL-EBI Homeobox 4.2E-29
Sequence
Target Sequence 
>C. ELEGANS:194012_S_AT
gtatggttctcgaatcggcgggcaaaatggaggagagaggaaaagatgagaaacaagcga
tcatccggcaccatggattcatcattatccaatggaacgccaacgccaacgccgggatca
gtgactggaagtaacatgacaaatccgattggatctccggccagcacgccgaatcgattc
ccttccaacaattcggcaaatctaccgacaacaaactttgtgcctcaaacgagtcagatg
tatgctgggctcagtcagccagcaatggatccatattcatttggaattgccaatggtttt
tcaatggctccatatccacaagtaacagatttccaaccacatcacatgttccaaggaaga
tcgccgtatgatttcccatatccaagaatgccgaccaatgggcatggtttccaacaatca
atgagtccggcaacaacggcggtaggagacattccgacactttcttctggaatgagccta
ccggtttctgcagtgctcaattccattgacccgtctctgactcactcacaaatgcat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTATGGTTCTCGAATCGGCGGGCAA 74 457 799 Antisense
GATCATCCGGCACCATGGATTCATC 436 417 857 Antisense
GCCAACGCCGGGATCAGTGACTGGA 524 277 903 Antisense
GACAAATCCGATTGGATCTCCGGCC 650 365 936 Antisense
TTCCCTTCCAACAATTCGGCAAATC 698 695 976 Antisense
GATTTCCAACCACATCACATGTTCC 677 427 1126 Antisense
ATCGCCGTATGATTTCCCATATCCA 630 37 1158 Antisense
TAGGAGACATTCCGACACTTTCTTC 313 655 1241 Antisense
TCTTCTGGAATGAGCCTACCGGTTT 179 613 1261 Antisense
TACCGGTTTCTGCAGTGCTCAATTC 467 649 1277 Antisense
GTCTCTGACTCACTCACAAATGCAT 140 471 1311 Antisense
Sequence Source Affymetrix Proprietary Database