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[171854_x_at]

Description CEC3983_rc /REP_DB=TREMBL Accession /GB=C10398 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk145e8 : 3prime end, single read.
Cluster 6grp_high1_10_10 > 03      4grp_high_8_8 > 10      6grp_total > 34      4grp_total > 22      6grp_cgc > 34      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 131
1 2 3 4 range
A 214.4
(2.5)
P 		134.9
(-1.5)
A 		104.1
(-3)
P 		223.8
(3)
A 		120
B 234.6
(3)
P 		134
(-3)
P 		169.5
(-0.9)
P 		191.1
(0.4)
M 		101
C 205
(1.5)
P 		182.6
(0.3)
P 		124.9
(-3)
P 		231.3
(3)
P 		106
avr 218
(3) 		150.5
(-1.8) 		132.8
(-3) 		215.4
(2.8) 		85

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 137
1 2 3 4 5 6 range
A 224.7
(3)
P 		204.1
(2.1)
P 		195.5
(1.7)
P 		97.2
(-2.6)
P 		87.5
(-3)
P 		98.2
(-2.5)
P 		137
B 207.7
(2.7)
P 		202.8
(2.3)
P 		212.1
(3)
P 		144
(-2.3)
P 		135.6
(-3)
P 		169.1
(-0.4)
P 		77
C 217.1
(3)
P 		188.7
(0.5)
P 		155
(-2.4)
P 		148.6
(-3)
M 		180.4
(-0.2)
P 		163.2
(-1.7)
P 		69
avr 216.5
(3) 		198.5
(1.8) 		187.5
(1) 		129.9
(-3) 		134.5
(-2.7) 		143.5
(-2.1) 		87
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 51
1 2 3 4 range
A 78.1
(3)
P 		29.3
(-2.8)
A 		27.2
(-3)
P 		32.8
(-2.3)
A 		51
B 74.8
(3)
P 		33.1
(-3)
P 		39.3
(-2.1)
P 		40.7
(-1.9)
M 		42
C 67.8
(3)
P 		52.5
(-0.2)
P 		43.5
(-2.1)
P 		39
(-3)
P 		29
avr 73.6
(3) 		38.3
(-2.7) 		36.7
(-3) 		37.5
(-2.9) 		37

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 57
1 2 3 4 5 6 range
A 41.4
(-0.8)
P 		72.6
(3)
P 		42.6
(-0.7)
P 		24.7
(-2.9)
P 		26.4
(-2.7)
P 		23.9
(-3)
P 		49
B 72.3
(3)
P 		67.5
(2.2)
P 		51.5
(-0.6)
P 		38.1
(-3)
P 		55.1
(-0)
P 		63.1
(1.4)
P 		34
C 80.5
(3)
P 		57.6
(0.3)
P 		39.4
(-1.9)
P 		29.9
(-3)
M 		58.4
(0.4)
P 		54.6
(-0.1)
P 		51
avr 64.7
(2.8) 		65.9
(3) 		44.5
(-0.7) 		30.9
(-3) 		46.6
(-0.3) 		47.2
(-0.2) 		35
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171854_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27976
Sequence Type Exemplar sequence
Representative Public ID CEC3983 NCBI
Target Description CEC3983_rc /REP_DB=TREMBL Accession /GB=C10398 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk145e8 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_077924
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
SNAP00000000614 ENSEMBL cdna:SNAP chromosome:CEL140:X:13965737:13968550:-1 None
F48F7.4 ENSEMBL cdna:known chromosome:CEL140:X:13965657:13969488:-1 gene:F48F7.4 A 
GENEFINDER00000000623 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:13965737:13968550:-1 None
NM_077924 NCBI Caenorhabditis elegans Prion-like-(Q/N-rich)-domain-bearing protein family member (pqn-39) (pqn-39) mRNA, complete cds. A 
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:13965727-13966156(-) 91.3 91.3
Public Domain and Genome References
Gene Title
Gene Symbol pqn-39
Ensembl F48F7.4
Entrez Gene 181506 Entrez gene
SwissProt Q20576 EMBL-EBI
WormBase CE05891 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA93494 Hypothetical protein F48F7.4 [Caenorhabditis elegans] ref|NP_510325.1| Prion-like-(Q/N-rich)-domain-bearing protein family member (pqn-39) [Caenorhabditis elegans] 0.0
blast CAE63059 Hypothetical protein CBG07337 [Caenorhabditis briggsae] 1.0E-107
blast CAE63059 Hypothetical protein CBG07337 [Caenorhabditis briggsae] 1.0E-106
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_510325.1 1 13-35
F48F7.4 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:171854_X_AT
taccgaggtggatacactggtgggtatnctgcacctcctcggtatattgtncggccagtc
gaaacgcctgcgacaccaaaagaatcggagcaaagtagttcaacggaagtagacgatatg
gctaagaaggatgtcgaagaaagtgttcaagatactccaagtgcaaccgaaagcacagta
gagacaccagctgatcaaggcaagactcaggagcagaataaagattctgattcccaaaac
gccaagcaggaaccggtcgcagnnnnngctaatgaagaaataattgnaattctaccacca
aataccatagtacaaagtcctgatgcagctgcag

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TACCGAGGTGGATACACTGGTGGGT 219 625 15 Antisense
AAACGCCTGCGACACCAAAAGAATC 216 125 76 Antisense
ATCGGAGCAAAGTAGTTCAACGGAA 102 35 98 Antisense
GTTCAAGATACTCCAAGTGCAACCG 146 445 159 Antisense
GCAACCGAAAGCACAGTAGAGACAC 434 319 177 Antisense
GTAGAGACACCAGCTGATCAAGGCA 26 457 192 Antisense
GATCAAGGCAAGACTCAGGAGCAGA 649 421 207 Antisense
AAGATTCTGATTCCCAAAACGCCAA 4 155 235 Antisense
TCCCAAAACGCCAAGCAGGAACCGG 534 595 246 Antisense
AATTCTACCACCAAATACCATAGTA 256 175 302 Antisense
GTACAAAGTCCTGATGCAGCTGCAG 429 461 324 Antisense
Sequence Source Affymetrix Proprietary Database