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[175548_at]

Description AV175762_rc /REP_DB=TREMBL Accession /GB=AV175762 /CHR=3 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk463c10 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 41      6grp_high1_10_10 > 05      4grp_highest_8_8 > 61      4grp_high_8_8 > 18      6grp_highest_nonorm > 60      6grp_total > 15      4grp_total > 30      6grp_highest_sub > De      6grp_cgc > 31      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 198
1 2 3 4 range
A 422.3
(3)
P 		320.7
(-1.3)
P 		281
(-3)
P 		318.4
(-1.4)
P 		141
B 407.3
(2.2)
P 		276.9
(-1.8)
P 		237.1
(-3)
P 		434.8
(3)
P 		198
C 415.1
(3)
P 		322.2
(-0.6)
P 		258.5
(-3)
P 		368
(1.2)
P 		157
avr 414.9
(3) 		306.6
(-1.2) 		258.9
(-3) 		373.7
(1.4) 		156

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 426
1 2 3 4 5 6 range
A 622.1
(3)
P 		416.6
(0.1)
P 		319.5
(-1.3)
P 		263.5
(-2.1)
P 		308.4
(-1.5)
P 		199.2
(-3)
P 		423
B 537.2
(3)
P 		464.5
(1.6)
P 		359.7
(-0.5)
P 		327
(-1.1)
P 		238.9
(-2.8)
P 		229.1
(-3)
P 		308
C 476.8
(1.9)
P 		540.9
(3)
P 		320.7
(-0.8)
P 		338.1
(-0.5)
P 		224.9
(-2.5)
P 		196.6
(-3)
P 		344
avr 545.4
(3) 		474
(1.7) 		333.3
(-0.8) 		309.5
(-1.2) 		257.4
(-2.1) 		208.3
(-3) 		337
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 107
1 2 3 4 range
A 153.8
(3)
P 		69.6
(-1.7)
P 		73.5
(-1.5)
P 		46.6
(-3)
P 		107
B 129.9
(3)
P 		68.4
(-1.9)
P 		54.9
(-3)
P 		92.7
(0)
P 		75
C 137.4
(3)
P 		92.6
(-0.6)
P 		90.1
(-0.8)
P 		62.1
(-3)
P 		75
avr 140.4
(3) 		76.9
(-2.2) 		72.8
(-2.5) 		67.1
(-3) 		73

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 138
1 2 3 4 5 6 range
A 114.7
(1)
P 		148.2
(3)
P 		69.6
(-1.7)
P 		66.8
(-1.9)
P 		93.1
(-0.3)
P 		48.5
(-3)
P 		100
B 186.9
(3)
P 		154.6
(1.1)
P 		87.3
(-2.9)
P 		86.6
(-2.9)
P 		97.1
(-2.3)
P 		85.4
(-3)
P 		102
C 176.7
(3)
P 		165.1
(2.4)
P 		81.6
(-2.1)
P 		68
(-2.9)
P 		72.8
(-2.6)
P 		65.8
(-3)
P 		111
avr 159.4
(3) 		156
(2.8) 		79.5
(-2.2) 		73.8
(-2.5) 		87.7
(-1.6) 		66.6
(-3) 		93
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175548_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21056
Sequence Type Exemplar sequence
Representative Public ID AV175762 NCBI
Target Description AV175762_rc /REP_DB=TREMBL Accession /GB=AV175762 /CHR=3 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk463c10 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_065175(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065175 NCBI Caenorhabditis elegans C.Elegans Homeobox family member (ceh-44) (ceh-44) mRNA, complete cds. 11/11 None
Y54F10AM.4a ENSEMBL cdna:known chromosome:CEL140:III:2530608:2543015:1 gene:Y54F10AM.4 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
175372 3 1 NM_065174 176499_at (11)
NM_065175 175548_at (11), 176483_at (11)
NM_065176 176499_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:2542685-2542971(+) 100.0 100.0
Public Domain and Genome References
Ensembl Y54F10AM.4
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK29942 C.elegans homeobox protein 44, isoform a [Caenorhabditis elegans] ref|NP_497576.1| C.Elegans Homeobox family member (ceh-44) [Caenorhabditis elegans] 0.0
blast CAE65011 Hypothetical protein CBG09849 [Caenorhabditis briggsae] 0.0
blast AAN84834 C.elegans homeobox protein 44, isoform c [Caenorhabditis elegans] ref|NP_497577.2| C.Elegans Homeobox family member (ceh-44) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 4.99999987368938E-5
Pfam IPR001356 EMBL-EBI Homeobox 3.1E-10
Pfam IPR003350 EMBL-EBI Homeodomain protein CUT 9.3E-31
Pfam IPR003350 EMBL-EBI Homeodomain protein CUT 8.5E-38
Sequence
Target Sequence 
>C. ELEGANS:175548_AT
taggcatcgttgtgcctgaaacccccaaaagtggctggttccacgtattctaaccaagtt
gttcaattacttattcaatcaattatatgtattttttttagttcttttcccttcataaaa
tgtctgcctagactgcctgcctaggcacgtaggcaggcaggcagctacctaaatttcccg
atctccttttgcagctttcacttttcccccctcttataaccattccattctctaatcatt
gaccggt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TAGGCATCGTTGTGCCTGAAACCCC 357 601 16 Antisense
GCCTGAAACCCCCAAAAGTGGCTGG 57 265 29 Antisense
GTGGCTGGTTCCACGTATTCTAACC 568 491 46 Antisense
TTCCACGTATTCTAACCAAGTTGTT 332 697 54 Antisense
GTTCTTTTCCCTTCATAAAATGTCT 351 443 116 Antisense
TAAAATGTCTGCCTAGACTGCCTGC 645 639 131 Antisense
TAGACTGCCTGCCTAGGCACGTAGG 465 639 144 Antisense
TAGGCACGTAGGCAGGCAGGCAGCT 8 653 157 Antisense
CAGGCAGCTACCTAAATTTCCCGAT 354 207 173 Antisense
CTCTTATAACCATTCCATTCTCTAA 620 229 226 Antisense
TTCCATTCTCTAATCATTGACCGGT 633 697 238 Antisense
Sequence Source Affymetrix Proprietary Database