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[173801_at] Protein-tyrosine phosphatase

Description C48493 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F54C8.4 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C48493 /WB_GENE_ID=F54C8.4 /WP=CE00190 /CHR=3 /FEA=Genomic Cluster /DEF=Protein-tyrosine phosphatase; C.elegans cDNA clone yk457c12 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 97      6grp_high1_10_10 > 79      4grp_highest_8_8 > 37      4grp_high_8_8 > 01      6grp_highest_nonorm > 97      6grp_total > 59      4grp_total > 15      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 723
1 2 3 4 range
A 1041
(3)
P 		577.7
(-3)
P 		757.5
(-0.7)
P 		1035
(2.9)
P 		463
B 1224.1
(2.1)
P 		804.9
(-2.7)
P 		778.3
(-3)
P 		1300.3
(3)
P 		522
C 1070.5
(1.7)
P 		683.8
(-3)
P 		843.9
(-1)
P 		1173.6
(3)
P 		490
avr 1111.9
(2.3) 		688.8
(-3) 		793.2
(-1.7) 		1169.6
(3) 		481

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 865
1 2 3 4 5 6 range
A 1096.9
(1.2)
P 		999.7
(0)
P 		844.4
(-1.8)
P 		741.7
(-3)
P 		1184.6
(2.2)
P 		1252.2
(3)
P 		511
B 1071.8
(0.2)
P 		752.3
(-2.1)
P 		635.6
(-3)
P 		995.7
(-0.3)
P 		1073.1
(0.2)
P 		1443.8
(3)
P 		808
C 1158.7
(0.4)
P 		718.4
(-3)
P 		895.1
(-1.6)
P 		809.7
(-2.3)
P 		1050
(-0.5)
P 		1500.3
(3)
P 		782
avr 1109.1
(0.1) 		823.5
(-2.7) 		791.7
(-3) 		849
(-2.4) 		1102.6
(0.1) 		1398.8
(3) 		607
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 265
1 2 3 4 range
A 379
(3)
P 		125.4
(-3)
P 		198
(-1.3)
P 		151.5
(-2.4)
P 		254
B 390.4
(3)
P 		198.8
(-2.5)
P 		180.3
(-3)
P 		277.1
(-0.2)
P 		210
C 354.4
(3)
P 		196.6
(-3)
P 		294.1
(0.7)
P 		197.9
(-3)
P 		158
avr 374.6
(3) 		173.6
(-3) 		224.1
(-1.5) 		208.8
(-1.9) 		201

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 384
1 2 3 4 5 6 range
A 202.2
(-2.4)
P 		355.6
(2.9)
P 		183.9
(-3)
P 		188.1
(-2.9)
P 		357.5
(3)
P 		304.9
(1.2)
P 		174
B 372.9
(0.4)
P 		250.4
(-1.5)
P 		154.4
(-3)
P 		263.7
(-1.3)
P 		436
(1.4)
P 		538.4
(3)
P 		384
C 429.5
(1.7)
P 		219.2
(-2)
P 		227.8
(-1.9)
P 		162.8
(-3)
P 		339.8
(0.1)
P 		502.2
(3)
P 		339
avr 334.9
(0.4) 		275.1
(-1) 		188.7
(-3) 		204.9
(-2.6) 		377.8
(1.4) 		448.5
(3) 		260
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173801_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.23854
Sequence Type Exemplar sequence
Representative Public ID C48493 NCBI
Target Description C48493 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F54C8.4 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C48493 /WB_GENE_ID=F54C8.4 /WP=CE00190 /CHR=3 /FEA=Genomic Cluster /DEF=Protein-tyrosine phosphatase; C.elegans cDNA clone yk457c12 : 5prime 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_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
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:9441471-9443253(-) 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 CAE65217 Hypothetical protein CBG10092 [Caenorhabditis briggsae] 1.0E-137
blast CAE57881 Hypothetical protein CBG00927 [Caenorhabditis briggsae] 9.0E-34
Sequence
Target Sequence 
>C. ELEGANS:173801_AT
ccagagattaggaggcagtgcttcgttcttctattaaattttttagactttgtgaatcat
tttgctcaatcattttcgtctccacaatgttctccctgttcaacttttgatcttttatcg
ttccactcttgtacctgactttaaacgtgcactacgcac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCAGAGATTAGGAGGCAGTGCTTCG 518 261 1083 Antisense
TAGGAGGCAGTGCTTCGTTCTTCTA 317 653 1091 Antisense
TAGACTTTGTGAATCATTTTGCTCA 706 651 1126 Antisense
ATTTTGCTCAATCATTTTCGTCTCC 252 15 1141 Antisense
CTCAATCATTTTCGTCTCCACAATG 558 227 1147 Antisense
TCATTTTCGTCTCCACAATGTTCTC 473 619 1152 Antisense
TTCTCCCTGTTCAACTTTTGATCTT 536 693 1172 Antisense
TTTTGATCTTTTATCGTTCCACTCT 536 675 1187 Antisense
TTCCACTCTTGTACCTGACTTTAAA 298 701 1203 Antisense
TGTACCTGACTTTAAACGTGCACTA 253 559 1212 Antisense
CTGACTTTAAACGTGCACTACGCAC 207 237 1217 Antisense
Sequence Source Affymetrix Proprietary Database