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[172007_x_at]

Description CE172_rc /REP_DB=TREMBL Accession /GB=T00172 /FEA=Transcript Cluster /DEF=wEST00893 Early embryo, Stratagene (cat. no. 937007) Caenorhabditis elegans cDNA clone CEESC34, mRNA sequence.
Cluster 6grp_highest_10_10 > 62      6grp_high1_10_10 > 26      4grp_highest_8_8 > 15      4grp_high_8_8 > 14      6grp_highest_nonorm > 27      6grp_total > 26      4grp_total > 09      6grp_highest_sub > Cu      6grp_cgc > 05      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 8791
1 2 3 4 range
A 9600.9
(-3)
P 		9863.8
(-2.7)
P 		10032.8
(-2.5)
P 		15301
(3)
P 		5700
B 8042.4
(-3)
P 		9070.3
(-2)
P 		8593.9
(-2.5)
P 		14065.3
(3)
P 		6023
C 8971.7
(-3)
P 		8913.4
(-3)
P 		9461.8
(-2.6)
P 		16833.6
(3)
P 		7920
avr 8871.7
(-3) 		9282.5
(-2.6) 		9362.8
(-2.5) 		15400
(3) 		6528

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2425
1 2 3 4 5 6 range
A 7973.2
(2.2)
P 		8123
(2.7)
P 		8195.7
(3)
P 		6930.6
(-1.6)
P 		6529.7
(-3)
P 		7446.5
(0.3)
P 		1666
B 8555.6
(3)
P 		8354.4
(2.5)
P 		6752.6
(-1.9)
P 		6340.9
(-3)
P 		6780.1
(-1.8)
P 		7789.8
(0.9)
P 		2215
C 8765.4
(3)
P 		7700.6
(0.2)
P 		7273.2
(-0.9)
P 		6454.5
(-3)
P 		8389.9
(2)
P 		6574.9
(-2.7)
P 		2311
avr 8431.4
(3) 		8059.3
(1.8) 		7407.2
(-0.3) 		6575.3
(-3) 		7233.2
(-0.9) 		7270.4
(-0.8) 		1856
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1504
1 2 3 4 range
A 3495.7
(3)
P 		2141.2
(-3)
P 		2622.8
(-0.9)
P 		2239.8
(-2.6)
P 		1355
B 2564.7
(0.4)
P 		2240.1
(-1.5)
P 		1991.4
(-3)
P 		2997.3
(3)
P 		1006
C 2969.9
(0.3)
P 		2562.6
(-3)
P 		3297.7
(3)
P 		2838.4
(-0.7)
P 		735
avr 3010.1
(3) 		2314.6
(-3) 		2637.3
(-0.2) 		2691.8
(0.3) 		696

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1951
1 2 3 4 5 6 range
A 1469.8
(-3)
P 		2888.9
(3)
P 		1784.8
(-1.7)
P 		1757.8
(-1.8)
P 		1970.4
(-0.9)
P 		1813
(-1.5)
P 		1419
B 2976.9
(3)
P 		2780.8
(2.1)
P 		1639.7
(-3)
P 		1679.5
(-2.8)
P 		2754.6
(2)
P 		2904.8
(2.7)
P 		1337
C 3249
(3)
P 		2349.7
(0.2)
P 		1851.2
(-1.3)
P 		1298
(-3)
P 		2714.8
(1.4)
P 		2201
(-0.2)
P 		1951
avr 2565.2
(2.4) 		2673.1
(3) 		1758.6
(-2) 		1578.4
(-3) 		2479.9
(1.9) 		2306.3
(1) 		1095
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172007_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27604
Sequence Type Exemplar sequence
Representative Public ID CE172 NCBI
Target Description CE172_rc /REP_DB=TREMBL Accession /GB=T00172 /FEA=Transcript Cluster /DEF=wEST00893 Early embryo, Stratagene (cat. no. 937007) Caenorhabditis elegans cDNA clone CEESC34, mRNA sequence.
Cluster Evidence This cluster is supported by a Transcript Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) U24123(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
U24123 NCBI Caenorhabditis elegans polyadenylate-binding protein mRNA, complete cds. 9/11 None
Y106G6H.2b.1 ENSEMBL cdna:known chromosome:CEL140:I:10440937:10443943:-1 gene:Y106G6H.2 9/11 A 
Y106G6H.2b.4 ENSEMBL cdna:known chromosome:CEL140:I:10440946:10443943:-1 gene:Y106G6H.2 9/11 A 
Y106G6H.2b.5 ENSEMBL cdna:known chromosome:CEL140:I:10440946:10443908:-1 gene:Y106G6H.2 9/11 A 
Y106G6H.2b.3 ENSEMBL cdna:known chromosome:CEL140:I:10440946:10443943:-1 gene:Y106G6H.2 9/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_001026539 8/11 Cross Hyb Matching Probes None
NM_001026538 6/11 Cross Hyb Matching Probes None
NM_001026540 6/11 Cross Hyb Matching Probes None
SNAP00000001702 6/11 Cross Hyb Matching Probes None
GENEFINDER00000001722 6/11 Cross Hyb Matching Probes None
Y106G6H.2b.6 8/11 Cross Hyb Matching Probes A 
Y106G6H.2b.2 8/11 Cross Hyb Matching Probes A 
Y106G6H.2a.5 6/11 Cross Hyb Matching Probes A 
Y106G6H.2a.1 6/11 Cross Hyb Matching Probes A 
Y106G6H.2a.3 6/11 Cross Hyb Matching Probes A 
Y106G6H.2a.2 6/11 Cross Hyb Matching Probes A 
Y106G6H.2a.4 6/11 Cross Hyb Matching Probes A 
Y106G6H.2c 6/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:10440932-10441190(-) 65.98 65.98
Public Domain and Genome References
Ensembl Y106G6H.2
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAA65224 polyadenylate-binding protein 0.0
blast CAA21572 Hypothetical protein Y106G6H.2a [Caenorhabditis elegans] ref|NP_001021709.1| PolyA Binding protein family member (pab-1) [Caenorhabditis elegans] 0.0
blast CAE58939 Hypothetical protein CBG02207 [Caenorhabditis briggsae] 0.0
blast CAE54916 Hypothetical protein Y106G6H.2b [Caenorhabditis elegans] ref|NP_001021710.1| PolyA Binding protein family member (pab-1) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002004 EMBL-EBI Polyadenylate-binding protein/HECT-associated 2.8E-28
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 6.1E-22
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 9.9E-23
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.1E-21
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 5.3E-24
Pfam IPR002004 EMBL-EBI Polyadenylate-binding protein/HECT-associated 2.8E-28
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 9.9E-23
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 5.3E-22
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 5.3E-24
Sequence
Target Sequence 
>C. ELEGANS:172007_X_AT
aatttccgagttgatcatgatgcttcaagatagtgaattgttccgctcgaaggtcgacga
agntgcatcggttttcgtttccgntcagaagcaataagtttcattgccaagtgtttntta
gcacgttccccnagttgctaagcataccnatcncctgnnnnnntntcttactgtcaccct
tcnnnnngttacttgttagtggttggtttagccgccccacannnnnnnnnnngagtaagc
tcacttttgtgatgtttattcac

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
AATTTCCGAGTTGATCATGATGCTT 112 175 92 Antisense
TCCGAGTTGATCATGATGCTTCAAG 704 595 96 Antisense
TGATCATGATGCTTCAAGATAGTGA 159 565 103 Antisense
CAAGATAGTGAATTGTTCCGCTCGA 175 185 117 Antisense
GATAGTGAATTGTTCCGCTCGAAGG 281 425 120 Antisense
TGAATTGTTCCGCTCGAAGGTCGAC 422 571 125 Antisense
TTGTTCCGCTCGAAGGTCGACGAAG 54 687 129 Antisense
CAATAAGTTTCATTGCCAAGTGTTT 308 181 183 Antisense
TACTTGTTAGTGGTTGGTTTAGCCG 251 583 281 Antisense
GAGTAAGCTCACTTTTGTGATGTTT 649 399 324 Antisense
GCTCACTTTTGTGATGTTTATTCAC 691 301 330 Antisense
Sequence Source Affymetrix Proprietary Database