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[192025_s_at] Protein-tyrosine phosphatase

Description F54C8.4 /REP_DB=WormBase Gene ID /WP=CE00190 /TR=SW:P34442 /GB=CAA80156.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Protein-tyrosine phosphatase
Cluster 6grp_highest_10_10 > 86      6grp_high1_10_10 > 78      4grp_highest_8_8 > 47      4grp_high_8_8 > 11      6grp_highest_nonorm > 94      6grp_total > 68      4grp_total > 21      6grp_highest_sub > Da      6grp_high1_sub > Cu      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 435
1 2 3 4 range
A 658.3
(0.1)
P 		462.5
(-2.6)
P 		436
(-3)
P 		870.8
(3)
P 		435
B 700.5
(1.7)
P 		526.9
(-2.5)
P 		506
(-3)
P 		752.2
(3)
P 		246
C 722.5
(2.4)
P 		694.6
(1.6)
P 		542.7
(-3)
P 		741.8
(3)
P 		199
avr 693.8
(1.1) 		561.3
(-1.6) 		494.9
(-3) 		788.3
(3) 		293

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 667
1 2 3 4 5 6 range
A 495
(-2.4)
P 		610.6
(-1.1)
P 		445.8
(-3)
P 		495.9
(-2.4)
P 		558.7
(-1.7)
P 		962.1
(3)
P 		516
B 600
(-0.7)
P 		379
(-3)
P 		513.4
(-1.6)
P 		471.3
(-2)
P 		623.7
(-0.4)
P 		952.8
(3)
P 		574
C 758.7
(0.4)
P 		387.9
(-3)
P 		520.5
(-1.8)
P 		419.2
(-2.7)
P 		608.9
(-1)
P 		1046.2
(3)
P 		658
avr 617.9
(-1.2) 		459.2
(-3) 		493.2
(-2.6) 		462.1
(-3) 		597.1
(-1.4) 		987
(3) 		528
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 139
1 2 3 4 range
A 239.7
(3)
P 		100.4
(-3)
P 		114
(-2.4)
P 		127.5
(-1.8)
P 		139
B 223.4
(3)
P 		130.1
(-2.3)
P 		117.2
(-3)
P 		160.3
(-0.6)
P 		106
C 239.2
(3)
P 		199.7
(0.9)
P 		189.2
(0.4)
P 		125.1
(-3)
P 		114
avr 234.1
(3) 		143.4
(-2.6) 		140.1
(-2.8) 		137.6
(-3) 		97

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 271
1 2 3 4 5 6 range
A 91.2
(-3)
P 		217.2
(2.3)
P 		97.1
(-2.8)
P 		125.8
(-1.5)
P 		168.6
(0.2)
P 		234.2
(3)
P 		143
B 208.8
(-0.8)
P 		126.1
(-3)
P 		124.7
(-3)
P 		124.8
(-3)
P 		253.4
(0.3)
P 		355.3
(3)
P 		231
C 281.2
(1.4)
P 		118.4
(-2.2)
P 		132.5
(-1.9)
P 		84.3
(-3)
P 		197
(-0.5)
P 		350.2
(3)
P 		266
avr 193.7
(-0.6) 		153.9
(-1.7) 		118.1
(-2.8) 		111.6
(-3) 		206.3
(-0.2) 		313.2
(3) 		202
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192025_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7968
Sequence Type Exemplar sequence
Representative Public ID F54C8.4 NCBI
Target Description F54C8.4 /REP_DB=WormBase Gene ID /WP=CE00190 /TR=SW:P34442 /GB=CAA80156.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Protein-tyrosine phosphatase
Cluster Evidence This cluster is supported by a 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_066675(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066675 NCBI Caenorhabditis elegans F54C8.4 (F54C8.4) mRNA, complete cds. 11/11 None
SNAP00000014862 ENSEMBL cdna:SNAP chromosome:CEL140:III:9441654:9443256:-1 11/11 None
GENEFINDER00000014873 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:9441654:9450193:-1 11/11 None
F54C8.4 ENSEMBL cdna:known chromosome:CEL140:III:9441465:9443475:-1 gene:F54C8.4 11/11 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
chrIII:9441649-9443252(-) 100.0 100.0
Public Domain and Genome References
Gene Title Protein-tyrosine phosphatase
Ensembl F54C8.4
Entrez Gene 176323 Entrez gene
SwissProt P34442 EMBL-EBI
WormBase CE00190 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6470 protein amino acid dephosphorylation inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4721 phosphoprotein phosphatase activity inferred from electronic annotation QuickGO AmiGO
8138 protein tyrosine/serine/threonine phosphatase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA80156 Hypothetical protein F54C8.4 [Caenorhabditis elegans] ref|NP_499076.1| F54C8.4 [Caenorhabditis elegans] sp|P34442|PTP4_CAEEL Probable tyrosine-protein phosphatase F54C8.4 1.0E-180
blast CAA80156 Hypothetical protein F54C8.4 [Caenorhabditis elegans] ref|NP_499076.1| F54C8.4 [Caenorhabditis elegans] sp|P34442|PTP4_CAEEL Probable tyrosine-protein phosphatase F54C8.4 1.0E-173
blast CAE65217 Hypothetical protein CBG10092 [Caenorhabditis briggsae] 1.0E-137
blast CAA80158 Hypothetical protein F54C8.6 [Caenorhabditis elegans] ref|NP_499077.1| F54C8.6 [Caenorhabditis elegans] sp|P34444|YL86_CAEEL Hypothetical protein F54C8.6 in chromosome III 1.0E-132
blast S40748 hypothetical protein F54C8.6 - Caenorhabditis elegans 1.0E-132
blast CAE57881 Hypothetical protein CBG00927 [Caenorhabditis briggsae] 9.0E-34
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000014873 2 189-211,324-346
Sequence
Target Sequence 
>C. ELEGANS:192025_S_AT
gacgcattcgaacaagccagaggatattcgattgaaaagggagcatatgtgatggctttg
cacaaggctgctaaagacaagcgagataaacaagtggattcggattccgactcgtctgag
cgccaaagaaagaagaagaataagagaaaacaccgtgaaattgtggaacatgaaaatatt
gtgctcattaatacaattattggcgagttgggaagtcaagctgccagcgtatctggaacc
gactatcaaaattcaccaaacggagtatccgtggacccaggacaaccacaaccgcaccac
tggggattcgctatcaagagatcgaaatacgctcaactcaatcaacctgttgcaaacgga
gccaatacaccacctgagccgtcagaagga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACGCATTCGAACAAGCCAGAGGAT 407 379 487 Antisense
GTGATGGCTTTGCACAAGGCTGCTA 662 483 535 Antisense
GTGGATTCGGATTCCGACTCGTCTG 270 489 580 Antisense
GACTCGTCTGAGCGCCAAAGAAAGA 223 375 595 Antisense
GGCGAGTTGGGAAGTCAAGCTGCCA 164 541 688 Antisense
GTCAAGCTGCCAGCGTATCTGGAAC 87 465 701 Antisense
GGAACCGACTATCAAAATTCACCAA 489 527 721 Antisense
CACCACTGGGGATTCGCTATCAAGA 364 201 781 Antisense
GAAATACGCTCAACTCAATCAACCT 375 361 810 Antisense
TGCAAACGGAGCCAATACACCACCT 233 577 837 Antisense
TACACCACCTGAGCCGTCAGAAGGA 391 643 852 Antisense
Sequence Source Affymetrix Proprietary Database