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[191898_at] Protein-tyrosine phosphatase

Description Y44A6D.4 /REP_DB=WormBase Gene ID /WP=CE19162 /TR=Q9XXD9 /GB=CAA19518.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=Protein-tyrosine phosphatase
Cluster 6grp_total > 22      4grp_total > 44      6grp_cgc > 61      6grp_cgc_sub > De      6grp_total_sub > Hat      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 67
1 2 3 4 range
A 35.8
(0)
A 		68.9
(3)
A 		2.3
(-3)
A 		21.5
(-1.3)
A 		67
B 62.8
(3)
M 		61
(2.8)
A 		19.2
(-2)
A 		10.7
(-3)
A 		52
C 46.6
(-0.3)
A 		62
(3)
A 		34.1
(-3)
A 		36.4
(-2.5)
A 		28
avr 48.4
(0.9) 		64
(3) 		18.5
(-3) 		22.9
(-2.4) 		46

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 51
1 2 3 4 5 6 range
A 32.6
(1.2)
A 		24.7
(-0.1)
A 		43.3
(3)
A 		6.9
(-3)
A 		32.7
(1.3)
A 		22
(-0.5)
A 		36
B 28.9
(2)
M 		25.8
(1.3)
A 		7.2
(-3)
A 		32
(2.7)
A 		33.2
(3)
A 		11.8
(-1.9)
A 		26
C 41.3
(1.5)
A 		54
(3)
P 		43
(1.7)
A 		28.6
(0)
A 		2.8
(-3)
A 		4.3
(-2.8)
A 		51
avr 34.3
(2.9) 		34.8
(3) 		31.2
(2) 		22.5
(-0.3) 		22.9
(-0.2) 		12.7
(-3) 		22
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 19
1 2 3 4 range
A 13
(2.2)
A 		15
(3)
A 		0.6
(-3)
A 		3.1
(-2)
A 		14
B 20
(3)
M 		15.1
(1.3)
A 		4.4
(-2.3)
A 		2.3
(-3)
A 		18
C 15.4
(1.8)
A 		17.8
(3)
A 		11.9
(-0)
A 		6.1
(-3)
A 		12
avr 16.1
(3) 		16
(3) 		5.6
(-2.1) 		3.8
(-3) 		12

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 16
1 2 3 4 5 6 range
A 6
(0.1)
A 		8.8
(2.2)
A 		9.4
(2.6)
A 		1.8
(-3)
A 		9.9
(3)
A 		5.3
(-0.4)
A 		8
B 10.1
(1.3)
M 		8.6
(0.5)
A 		1.7
(-3)
A 		8.5
(0.5)
A 		13.5
(3)
A 		4.4
(-1.6)
A 		12
C 15.3
(2.5)
A 		16.5
(3)
P 		10.9
(0.8)
A 		5.8
(-1.1)
A 		0.9
(-3)
A 		1.4
(-2.8)
A 		16
avr 10.5
(2.4) 		11.3
(3) 		7.3
(-0.2) 		5.4
(-1.7) 		8.1
(0.5) 		3.7
(-3) 		8
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191898_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14715
Sequence Type Exemplar sequence
Representative Public ID Y44A6D.4 NCBI
Target Description Y44A6D.4 /REP_DB=WormBase Gene ID /WP=CE19162 /TR=Q9XXD9 /GB=CAA19518.1 /SUBMIT=HINXTON /CHR=5 /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_075612(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075612 NCBI Caenorhabditis elegans Synthetic Dauer Formation family member (sdf-9) (sdf-9) mRNA, complete cds. 11/11 None
SNAP00000040629 ENSEMBL cdna:SNAP chromosome:CEL140:V:20796263:20799017:1 10/11 None
GENEFINDER00000040636 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:20796263:20798602:1 11/11 None
Y44A6D.4 ENSEMBL cdna:known chromosome:CEL140:V:20796269:20799258:1 gene:Y44A6D.4 11/11 None
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
chrV:20796262-20798428(+) 99.64 100.0
Public Domain and Genome References
Gene Title Protein-tyrosine phosphatase
Gene Symbol sdf-9
Ensembl Y44A6D.4
Entrez Gene 189901 Entrez gene
SwissProt Q9XXD9 EMBL-EBI
WormBase CE35663 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
4725 protein tyrosine phosphatase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA19518 Hypothetical protein Y44A6D.4 [Caenorhabditis elegans] ref|NP_508013.2| Synthetic Dauer Formation family member (sdf-9) [Caenorhabditis elegans] dbj|BAC75705.1| SDF-9 protein [Caenorhabditis elegans] 0.0
blast CAA19518 Hypothetical protein Y44A6D.4 [Caenorhabditis elegans] ref|NP_508013.2| Synthetic Dauer Formation family member (sdf-9) [Caenorhabditis elegans] dbj|BAC75705.1| SDF-9 protein [Caenorhabditis elegans] 1.0E-176
blast CAB02281 Hypothetical protein F10G8.4 [Caenorhabditis elegans] ref|NP_492649.1| F10G8.4 [Caenorhabditis elegans] 2.0E-49
blast CAB02281 Hypothetical protein F10G8.4 [Caenorhabditis elegans] ref|NP_492649.1| F10G8.4 [Caenorhabditis elegans] 1.0E-47
blast CAB02281 Hypothetical protein F10G8.4 [Caenorhabditis elegans] ref|NP_492649.1| F10G8.4 [Caenorhabditis elegans] 5.0E-39
blast XP_695831 PREDICTED: similar to protein tyrosine phosphatase e [Danio rerio] 7.0E-17
blast XP_695831 PREDICTED: similar to protein tyrosine phosphatase e [Danio rerio] 1.0E-16
Protein Domains
Database ID Description E-Value
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 1.6E-55
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 3.5E-43
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 1.6E-55
Sequence
Target Sequence 
>C. ELEGANS:191898_AT
catcagggaaactttcacacccggaattttattcttagaaaaggaaacgaaactcaccga
gttctgcattttacagtctttggatggactgaaactacaacaccaataatgcaagatttt
ttggctttgcggaaagtaatgaaagacacgggggcgctcaatatgatcaatccagcaagt
gcactcttcaggtccacaatgcgccggtacattcacactcctccatcttttgctccaatc
attcaaagtgcaagaggaagtagccgagctggagcatttgttgtcattgatcttctcata
cgtatgattgatggcaagaaaactaatctgtattcagtggaggatctcatcgtgaagtgc
aaacacatgagaattcattgcgttccagtggctttgcaccattcgttcatttatgaagct
gttctagactatcttcttag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CATCAGGGAAACTTTCACACCCGGA 177 185 493 Antisense
AAACTCACCGAGTTCTGCATTTTAC 608 127 542 Antisense
GACACGGGGGCGCTCAATATGATCA 506 367 637 Antisense
ATCCAGCAAGTGCACTCTTCAGGTC 605 39 662 Antisense
TCCATCTTTTGCTCCAATCATTCAA 508 591 714 Antisense
CCGAGCTGGAGCATTTGTTGTCATT 690 263 756 Antisense
GTTGTCATTGATCTTCTCATACGTA 502 437 772 Antisense
GTGGAGGATCTCATCGTGAAGTGCA 68 491 829 Antisense
AATTCATTGCGTTCCAGTGGCTTTG 528 175 864 Antisense
TGGCTTTGCACCATTCGTTCATTTA 142 545 881 Antisense
AAGCTGTTCTAGACTATCTTCTTAG 85 151 908 Antisense
Sequence Source Affymetrix Proprietary Database