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[180024_s_at]

Description Y39E4B.3 /REP_DB=WormBase Gene ID /WP=CE21715 /TR=Q9U2K1 /GB=CAB54432.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 04      6grp_high1_10_10 > 21      4grp_highest_8_8 > 49      4grp_high_8_8 > 41      6grp_highest_nonorm > 42      6grp_total > 32      4grp_total > 54      6grp_cgc > 70      6grp_high1_sub > 03      6grp_total_sub > Hat      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 487
1 2 3 4 range
A 982.1
(3)
P 		654.3
(-1.5)
P 		558.8
(-2.8)
P 		544.4
(-3)
P 		438
B 752.5
(2.8)
P 		759.1
(3)
P 		623.8
(-0.5)
P 		526.2
(-3)
P 		233
C 1010.5
(3)
P 		601.9
(-2)
P 		694.2
(-0.9)
P 		523.1
(-3)
P 		487
avr 915
(3) 		671.8
(-0.8) 		625.6
(-1.5) 		531.2
(-3) 		384

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 724
1 2 3 4 5 6 range
A 619
(-1.8)
P 		758.1
(0)
P 		986.7
(3)
P 		825.9
(0.9)
P 		635.6
(-1.5)
P 		523.5
(-3)
P 		463
B 790.7
(1)
P 		755.4
(0.5)
P 		948.3
(3)
P 		706.4
(-0.1)
P 		731.5
(0.2)
P 		482.9
(-3)
P 		465
C 1036.4
(2.5)
P 		724.5
(-0.1)
P 		863.2
(1)
P 		671.7
(-0.5)
P 		1099.5
(3)
P 		375.2
(-3)
P 		724
avr 815.4
(1.5) 		746
(0.6) 		932.7
(3) 		734.7
(0.5) 		822.2
(1.6) 		460.5
(-3) 		472
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 278
1 2 3 4 range
A 357.6
(3)
P 		142
(-1.7)
P 		146.1
(-1.6)
P 		79.7
(-3)
P 		278
B 240
(3)
P 		187.5
(0.5)
P 		144.5
(-1.5)
P 		112.1
(-3)
P 		128
C 334.5
(3)
P 		173.1
(-0.9)
P 		241.9
(0.7)
P 		88.2
(-3)
P 		246
avr 310.7
(3) 		167.5
(-1) 		177.5
(-0.7) 		93.3
(-3) 		217

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 270
1 2 3 4 5 6 range
A 114.1
(-3)
P 		269.6
(3)
P 		214.9
(0.9)
P 		209.5
(0.7)
P 		191.8
(-0)
P 		127.5
(-2.5)
P 		156
B 275.1
(1.9)
P 		251.4
(0.7)
P 		230.3
(-0.4)
P 		187.1
(-2.6)
P 		297.2
(3)
P 		180.1
(-3)
P 		117
C 384.1
(3)
P 		221.1
(-0.8)
P 		219.7
(-0.8)
P 		135.1
(-2.8)
P 		355.8
(2.3)
P 		125.6
(-3)
P 		259
avr 257.8
(2) 		247.4
(1.5) 		221.6
(0.4) 		177.2
(-1.6) 		281.6
(3) 		144.4
(-3) 		137
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 180024_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6351
Sequence Type Exemplar sequence
Representative Public ID Y39E4B.3 NCBI
Target Description Y39E4B.3 /REP_DB=WormBase Gene ID /WP=CE21715 /TR=Q9U2K1 /GB=CAB54432.1 /SUBMIT=HINXTON /CHR=3 /FEA=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_001027682(11), NM_001027683(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027682 NCBI Caenorhabditis elegans Prion-like-(Q/N-rich)-domain-bearing protein family member (pqn-83) (pqn-83) mRNA, complete cds. 11/11 None
NM_001027683 NCBI Caenorhabditis elegans Prion-like-(Q/N-rich)-domain-bearing protein family member (pqn-83) (pqn-83) mRNA, complete cds. 11/11 None
Y39E4B.3a ENSEMBL cdna:known chromosome:CEL140:III:13087007:13098971:-1 gene:Y39E4B.3 11/11 A 
Y39E4B.3b ENSEMBL cdna:known chromosome:CEL140:III:13087008:13098971:-1 gene:Y39E4B.3 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_001027684 4/11 Cross Hyb Matching Probes None
SNAP00000012007 2/11 Cross Hyb Matching Probes None
GENEFINDER00000012031 7/11 Cross Hyb Matching Probes None
SNAP00000012009 4/11 Cross Hyb Matching Probes None
GENEFINDER00000012024 4/11 Cross Hyb Matching Probes None
GENEFINDER00000012038 2/11 Cross Hyb Matching Probes None
Y39E4B.3c.2 4/11 Cross Hyb Matching Probes None
Y39E4B.3c.1 4/11 Cross Hyb Matching Probes None
Y39E4B.14 2/11 Cross Hyb Matching Probes None
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
176729 3 2 NM_001027682 171951_x_at (10), 180024_s_at (11), 194174_x_at (9)
NM_001027683 171951_x_at (9), 180024_s_at (11), 194174_x_at (10)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:13087254-13098967(-) 92.68 100.0
Public Domain and Genome References
Ensembl Y39E4B.3
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAH10817 Hypothetical protein Y39E4B.3b [Caenorhabditis elegans] ref|NP_001022854.1| Prion-like-(Q/N-rich)-domain-bearing protein family member (pqn-83) [Caenorhabditis elegans] 6.0E-76
blast CAH10818 Hypothetical protein Y39E4B.3c [Caenorhabditis elegans] ref|NP_001022855.1| Prion-like-(Q/N-rich)-domain-bearing protein family member (pqn-83) [Caenorhabditis elegans] 4.0E-68
blast CAB54432 Hypothetical protein Y39E4B.3a [Caenorhabditis elegans] ref|NP_001022853.1| Prion-like-(Q/N-rich)-domain-bearing protein family member (pqn-83) [Caenorhabditis elegans] 1.0E-67
blast CAB54432 Hypothetical protein Y39E4B.3a [Caenorhabditis elegans] ref|NP_001022853.1| Prion-like-(Q/N-rich)-domain-bearing protein family member (pqn-83) [Caenorhabditis elegans] 7.0E-67
blast CAH10818 Hypothetical protein Y39E4B.3c [Caenorhabditis elegans] ref|NP_001022855.1| Prion-like-(Q/N-rich)-domain-bearing protein family member (pqn-83) [Caenorhabditis elegans] 2.0E-66
blast CAH10817 Hypothetical protein Y39E4B.3b [Caenorhabditis elegans] ref|NP_001022854.1| Prion-like-(Q/N-rich)-domain-bearing protein family member (pqn-83) [Caenorhabditis elegans] 2.0E-66
Protein Domains
Database ID Description E-Value
Pfam IPR002619 EMBL-EBI Protein of unknown function CX 1.7E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001022853.1 1 291-313
Y39E4B.3a 1 291-313
Sequence
Target Sequence 
>C. ELEGANS:180024_S_AT
cagtgctcaattccgttgagccagttgaccgcgcagcaatccaccaccaccaccacaccg
acaacaacatcgacaacgacagcctctccagatggttcaacgacgatttctccatcatca
actactccaacaccggagcaggttcttcaaaatatccaataccccgacggatcgcgaccg
aagaacattgtatgggcatgcaaagccggacgtgaagtgtgctgtggaaccgactgctgt
ccggctccagttcaaaaccaaaattctgccggaggagccggtggaagtcacggatccggt
ggatcggctggaaccatcgcactcattgtcatcattatccttcttctcctctgctgtgga
tgctgcctgggtgcctatttctgttgccgatcgattttcgattgtggagatgataagcgt
gacgatcaacagtatcatgatgattattcccaacaacaacaatatcaaatgcaaaactat
ccaccacaacaacagcagcaacagcaatacggacaatattatcaacaaccacagcaaggc
ggttattcacagcagcagc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGTGCTCAATTCCGTTGAGCCAGT 63 209 571 Antisense
TCAATTCCGTTGAGCCAGTTGACCG 59 635 577 Antisense
ACCACACCGACAACAACATCGACAA 375 85 622 Antisense
ACAACAACATCGACAACGACAGCCT 671 111 631 Antisense
CTATTTCTGTTGCCGATCGATTTTC 281 223 945 Antisense
GTTGCCGATCGATTTTCGATTGTGG 619 439 953 Antisense
GATTGTGGAGATGATAAGCGTGACG 208 435 970 Antisense
AAGCGTGACGATCAACAGTATCATG 6 151 985 Antisense
CATGATGATTATTCCCAACAACAAC 281 211 1006 Antisense
AATGCAAAACTATCCACCACAACAA 231 165 1038 Antisense
CAAGGCGGTTATTCACAGCAGCAGC 668 183 1105 Antisense
Sequence Source Affymetrix Proprietary Database