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[173882_s_at]

Description CEK006B5R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F18H3.3A /5_PRIME_EXT_DB=WormBase Gene ID /GB=D27926 /WB_GENE_ID=F18H3.3A /WP=CE02193 /CHR=X /FEA=Genomic Cluster /DEF=poly-adenylate binding protein; C.elegans cDNA clone yk6b5 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 19      6grp_high1_10_10 > 09      4grp_highest_8_8 > 23      4grp_high_8_8 > 06      6grp_highest_nonorm > 38      6grp_total > 92      4grp_total > 02      6grp_highest_sub > 05      6grp_cgc > 97      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 15759
1 2 3 4 range
A 4055.3
(-2.4)
P 		2580.4
(-3)
P 		2842.7
(-2.9)
P 		17236.3
(3)
P 		14656
B 3537.9
(-2.4)
P 		2333.4
(-3)
P 		2468.2
(-2.9)
P 		14929.4
(3)
P 		12596
C 3567.2
(-2.6)
P 		2658
(-3)
P 		2941.9
(-2.9)
P 		18092.7
(3)
P 		15435
avr 3720.1
(-2.5) 		2523.9
(-3) 		2750.9
(-2.9) 		16752.8
(3) 		14229

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4974
1 2 3 4 5 6 range
A 5569.4
(-2.1)
P 		5761.7
(-1.7)
P 		5205.2
(-3)
P 		7690.9
(3)
P 		6845.4
(1)
P 		6230.8
(-0.5)
P 		2486
B 7629.8
(2.7)
P 		5702.9
(-0.8)
P 		4501
(-3)
P 		7811.2
(3)
P 		6178.2
(0)
P 		6034.6
(-0.2)
P 		3310
C 6585.6
(-0.3)
P 		6137.6
(-0.8)
P 		5438.7
(-1.6)
P 		4942.5
(-2.2)
P 		9280.7
(3)
P 		4306.5
(-3)
P 		4974
avr 6594.9
(0.9) 		5867.4
(-0.9) 		5048.3
(-3) 		6814.9
(1.4) 		7434.8
(3) 		5524
(-1.8) 		2387
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2621
1 2 3 4 range
A 1476.5
(-0.2)
P 		560.1
(-3)
P 		743.1
(-2.4)
P 		2523.1
(3)
P 		1963
B 1128.2
(-1.7)
P 		576.3
(-3)
P 		571.9
(-3)
P 		3181.5
(3)
P 		2610
C 1180.8
(-1.9)
P 		764.2
(-3)
P 		1025.3
(-2.3)
P 		3050.7
(3)
P 		2287
avr 1261.8
(-1.4) 		633.5
(-3) 		780.1
(-2.6) 		2918.4
(3) 		2285

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2009
1 2 3 4 5 6 range
A 1026.7
(-3)
P 		2049.2
(2.9)
P 		1133.6
(-2.4)
P 		1950.6
(2.3)
P 		2065.7
(3)
P 		1517
(-0.2)
P 		1039
B 2654.8
(3)
P 		1898.3
(0.1)
P 		1093
(-3)
P 		2068.9
(0.7)
P 		2510.1
(2.4)
P 		2250.3
(1.4)
P 		1562
C 2441
(1.3)
P 		1872.8
(-0.4)
P 		1384.2
(-1.8)
P 		993.9
(-3)
P 		3003.1
(3)
P 		1441.7
(-1.7)
P 		2009
avr 2040.8
(0.8) 		1940.1
(0.3) 		1203.6
(-3) 		1671.1
(-0.9) 		2526.3
(3) 		1736.3
(-0.6) 		1323
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173882_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26058
Sequence Type Exemplar sequence
Representative Public ID CEK006B5R NCBI
Target Description CEK006B5R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F18H3.3A /5_PRIME_EXT_DB=WormBase Gene ID /GB=D27926 /WB_GENE_ID=F18H3.3A /WP=CE02193 /CHR=X /FEA=Genomic Cluster /DEF=poly-adenylate binding protein; C.elegans cDNA clone yk6b5 : 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_077859(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077859 NCBI Caenorhabditis elegans PolyA Binding protein family member (pab-2) (pab-2) mRNA, complete cds. 11/11 A 
SNAP00000001958 ENSEMBL cdna:SNAP chromosome:CEL140:X:13523124:13525738:-1 11/11 None
GENEFINDER00000001960 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:13523124:13525738:-1 11/11 None
F18H3.3a.3 ENSEMBL cdna:known chromosome:CEL140:X:13522198:13527285:-1 gene:F18H3.3 11/11 A 
F18H3.3a.4 ENSEMBL cdna:known chromosome:CEL140:X:13522198:13525742:-1 gene:F18H3.3 11/11 A 
F18H3.3a.1 ENSEMBL cdna:known chromosome:CEL140:X:13522198:13527334:-1 gene:F18H3.3 11/11 A 
F18H3.3a.2 ENSEMBL cdna:known chromosome:CEL140:X:13522198:13527274:-1 gene:F18H3.3 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
181473 2 1 NM_077858 174888_at (11)
NM_077859 173881_at (11), 173882_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:13522834-13525739(-) 100.0 100.0
Public Domain and Genome References
Ensembl F18H3.3
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA90444 Hypothetical protein F18H3.3a [Caenorhabditis elegans] ref|NP_510260.1| PolyA Binding protein family member (pab-2) [Caenorhabditis elegans] 0.0
blast CAE63132 Hypothetical protein CBG07431 [Caenorhabditis briggsae] 0.0
blast CAA90446 Hypothetical protein F18H3.3b [Caenorhabditis elegans] ref|NP_510259.1| PolyA Binding protein family member (pab-2) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002004 EMBL-EBI Polyadenylate-binding protein/HECT-associated 1.9E-29
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.5E-21
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 6.6E-21
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 5.6E-22
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 4.0E-25
Sequence
Target Sequence 
>C. ELEGANS:173882_S_AT
gacaatccggaatcgttattcacggacaggagactcttacctcccatatgcttgctcaag
ctgctccacaagagcaaaagcaacttctcggagagcgtatctatgctcttatcgagaaga
tgttcccgaaccacaaggaggccggcaaaatcactggaatgatgctggagattgacaacg
ccgagttgatcatgatgctccaagacgctgagttgttcagaagcaaggtcgaggaagcct
ttggagtgctcaccaatgctcagagtgctgctgcttctacttctgctccaactgctaaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACAATCCGGAATCGTTATTCACGG 357 365 1788 Antisense
CACGGACAGGAGACTCTTACCTCCC 321 199 1808 Antisense
ATATGCTTGCTCAAGCTGCTCCACA 523 21 1833 Antisense
GCAAAAGCAACTTCTCGGAGAGCGT 277 319 1861 Antisense
GAGCGTATCTATGCTCTTATCGAGA 290 387 1880 Antisense
TTCCCGAACCACAAGGAGGCCGGCA 636 695 1910 Antisense
GATGCTGGAGATTGACAACGCCGAG 34 415 1948 Antisense
GATGCTCCAAGACGCTGAGTTGTTC 78 415 1981 Antisense
GAGGAAGCCTTTGGAGTGCTCACCA 480 405 2018 Antisense
AATGCTCAGAGTGCTGCTGCTTCTA 97 167 2042 Antisense
TCTACTTCTGCTCCAACTGCTAAAA 183 615 2063 Antisense
Sequence Source Affymetrix Proprietary Database