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[175692_s_at]

Description g965065 /REP_DB=GenBank Identifier /GB=U31537.1 /PROTEIN_GB=AAA82991.1 /CHR=X /FEA=Mapped Transcript /DEF=variable abnormal-3
Cluster 6grp_highest_10_10 > 60      6grp_high1_10_10 > 16      4grp_highest_8_8 > 58      4grp_high_8_8 > 33      6grp_highest_nonorm > 50      6grp_total > 06      4grp_total > 46      6grp_highest_sub > De      6grp_cgc > 13      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 696
1 2 3 4 range
A 965.5
(3)
P 		381.8
(-2.7)
P 		348.7
(-3)
P 		357.3
(-2.9)
P 		617
B 811.2
(3)
P 		505.1
(-0.4)
P 		269.1
(-3)
P 		375.6
(-1.8)
P 		542
C 831.7
(3)
P 		406.7
(-1.6)
P 		283.3
(-3)
P 		354.5
(-2.2)
P 		548
avr 869.5
(3) 		431.2
(-1.6) 		300.4
(-3) 		362.5
(-2.3) 		569

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 712
1 2 3 4 5 6 range
A 985.2
(3)
P 		685.8
(0.3)
P 		338.7
(-2.7)
P 		395
(-2.2)
P 		423.8
(-2)
P 		307.9
(-3)
P 		677
B 779.1
(3)
P 		600.2
(0.9)
P 		281.5
(-2.9)
P 		486
(-0.5)
P 		323.4
(-2.4)
P 		273.1
(-3)
P 		506
C 698.6
(3)
P 		574.7
(0.8)
P 		464.1
(-1.1)
P 		401.1
(-2.2)
P 		357
(-3)
P 		382.7
(-2.5)
P 		342
avr 821
(3) 		620.2
(0.6) 		361.4
(-2.5) 		427.4
(-1.7) 		368.1
(-2.4) 		321.2
(-3) 		500
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 299
1 2 3 4 range
A 351.5
(3)
P 		82.9
(-2.4)
P 		91.2
(-2.2)
P 		52.3
(-3)
P 		299
B 258.7
(3)
P 		124.7
(-1.1)
P 		62.4
(-3)
P 		80
(-2.5)
P 		196
C 275.3
(3)
P 		116.9
(-1.4)
P 		98.8
(-1.9)
P 		59.8
(-3)
P 		216
avr 295.2
(3) 		108.2
(-1.9) 		84.1
(-2.5) 		64
(-3) 		231

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 203
1 2 3 4 5 6 range
A 181.6
(0.8)
P 		243.9
(3)
P 		73.8
(-3)
P 		100.2
(-2.1)
P 		127.9
(-1.1)
P 		75
(-3)
P 		170
B 271.1
(3)
P 		199.8
(0.9)
P 		68.3
(-3)
P 		128.7
(-1.2)
P 		131.4
(-1.1)
P 		101.8
(-2)
P 		203
C 258.9
(3)
P 		175.4
(0.2)
P 		118.1
(-1.7)
P 		80.7
(-3)
P 		115.5
(-1.8)
P 		128.1
(-1.4)
P 		178
avr 237.2
(3) 		206.4
(1.8) 		86.7
(-3) 		103.2
(-2.3) 		124.9
(-1.5) 		101.6
(-2.4) 		151
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175692_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19986
Sequence Type Exemplar sequence
Representative Public ID 965065 NCBI
Target Description g965065 /REP_DB=GenBank Identifier /GB=U31537.1 /PROTEIN_GB=AAA82991.1 /CHR=X /FEA=Mapped Transcript /DEF=variable abnormal-3
Cluster Evidence This cluster is supported by a Mapped Transcript.
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_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_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
F14F3.1a ENSEMBL cdna:known chromosome:CEL140:X:10499862:10519502:1 gene:F14F3.1 11/11 A 
F14F3.1c ENSEMBL cdna:known chromosome:CEL140:X:10515914:10519502:1 gene:F14F3.1 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
181251 3 2 NM_001029399 175692_s_at (11)
NM_001029401 175692_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:10499861-10519502(+) 100.0 100.0
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 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.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
Sequence
Target Sequence 
>C. ELEGANS:175692_S_AT
ccctttttccttcattcatgagctgtcacatattcaatccccattcctttatgctagatt
ttgtagaccagtgacttttgttgtcccatttaaatggaacatgtagagtattgctctaca
gaatatcgtgcacaaaatgacatttgccccacgtccccccccccccctctccttaaattt
caaacttcttccagagttttcaattgtatcacatattttttattctgttgagcatgaaaa
ttgtttttccgttttcaaactatatattcttaggttcaactatacaattcaattgattat
gacatattgaaaacgaaaaaaaactgttgttatcattaactctgatttgtcagtattttc
tcaattttttaaaccttagaaatctacccactttccatgtagagtgtcaattaaatttta
tcttggagtgagcgattttggaacttatagtgaaaaatgaaaaagtttcaattgtttcat
atcatgcattctatctggttgttttctttttttccaaattttgaccatttccttcctctc
ttgaaccgttctctcattgttat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCCTTTTTCCTTCATTCATGAGCTG 505 259 1952 Antisense
TGAGCTGTCACATATTCAATCCCCA 294 569 1970 Antisense
ATCCCCATTCCTTTATGCTAGATTT 180 39 1988 Antisense
GACCAGTGACTTTTGTTGTCCCATT 661 383 2017 Antisense
ATTGCTCTACAGAATATCGTGCACA 679 5 2061 Antisense
CACAAAATGACATTTGCCCCACGTC 317 195 2082 Antisense
TCCTTAAATTTCAAACTTCTTCCAG 580 591 2121 Antisense
TAGAAATCTACCCACTTTCCATGTA 221 651 2328 Antisense
GTTTCATATCATGCATTCTATCTGG 84 451 2425 Antisense
CATTCTATCTGGTTGTTTTCTTTTT 25 217 2438 Antisense
TCTTGAACCGTTCTCTCATTGTTAT 565 615 2490 Antisense
Sequence Source GenBank