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[175530_s_at]

Description AV200589_rc /REP_DB=TREMBL Accession /GB=AV200589 /CHR=4 /FEA=Genomic Cluster /REVCOMP /DEF=Caenorhabditis elegans cDNA clone:yk577e5 : 3prime end, single read.
Cluster 6grp_total > 29      4grp_total > 28      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 35
1 2 3 4 range
A 21.3
(1)
A 		28.6
(3)
A 		6.7
(-3)
A 		9.8
(-2.2)
A 		22
B 23.9
(-0.1)
A 		6.5
(-3)
A 		20.4
(-0.6)
A 		41.9
(3)
A 		35
C 19.2
(-3)
A 		36.9
(3)
A 		25.9
(-0.7)
A 		25.2
(-1)
A 		18
avr 21.5
(-0.1) 		24
(1.8) 		17.7
(-3) 		25.6
(3) 		8

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 31
1 2 3 4 5 6 range
A 7
(-1.6)
A 		13
(0.5)
A 		19.8
(2.9)
A 		4.3
(-2.5)
A 		20.1
(3)
A 		3
(-3)
A 		17
B 29.7
(3)
A 		13.9
(-3)
A 		27.8
(2.3)
A 		19.9
(-0.7)
A 		21.6
(-0.1)
A 		17.8
(-1.5)
A 		16
C 34.4
(3)
A 		18.5
(-0.3)
A 		5.7
(-3)
A 		5.6
(-3)
A 		15.6
(-0.9)
A 		20.2
(0)
A 		29
avr 23.7
(3) 		15.1
(-0.7) 		17.8
(0.4) 		9.9
(-3) 		19.1
(1) 		13.7
(-1.3) 		14
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 9
1 2 3 4 range
A 7.7
(3)
A 		6.2
(1.6)
A 		1.8
(-2.6)
A 		1.4
(-3)
A 		6
B 7.6
(1.9)
A 		1.6
(-3)
A 		4.7
(-0.5)
A 		8.9
(3)
A 		7
C 6.3
(-1.1)
A 		10.6
(3)
A 		9
(1.5)
A 		4.3
(-3)
A 		6
avr 7.2
(3) 		6.1
(0.1) 		5.2
(-2.2) 		4.9
(-3) 		2

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 12
1 2 3 4 5 6 range
A 1.3
(-2.3)
A 		4.6
(1.3)
A 		4.3
(1)
A 		1.1
(-2.6)
A 		6.1
(3)
A 		0.7
(-3)
A 		5
B 10.3
(3)
A 		4.6
(-3)
A 		6.8
(-0.7)
A 		5.3
(-2.3)
A 		8.8
(1.4)
A 		6.6
(-0.9)
A 		6
C 12.8
(3)
A 		5.6
(-0.7)
A 		1.5
(-2.8)
A 		1.1
(-3)
A 		5
(-1)
A 		6.8
(-0.1)
A 		12
avr 8.1
(3) 		4.9
(-0.4) 		4.2
(-1.2) 		2.5
(-3) 		6.6
(1.4) 		4.7
(-0.6) 		6
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175530_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.28230
Sequence Type Exemplar sequence
Representative Public ID AV200589 NCBI
Target Description AV200589_rc /REP_DB=TREMBL Accession /GB=AV200589 /CHR=4 /FEA=Genomic Cluster /REVCOMP /DEF=Caenorhabditis elegans cDNA clone:yk577e5 : 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_067727(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067727 NCBI Caenorhabditis elegans Y41D4A.5 (Y41D4A.5) mRNA, complete cds. 11/11 None
SNAP00000028254 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1728418:1759946:-1 11/11 None
GENEFINDER00000028269 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1731157:1733463:-1 11/11 None
Y41D4A.5 ENSEMBL cdna:known chromosome:CEL140:IV:1728049:1737882:-1 gene:Y41D4A.5 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
chrIV:1733181-1733461(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl Y41D4A.5
Entrez Gene 176981 Entrez gene
WormBase CE39047 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFA.19703.1.S1_AT similar to protein tyrosine phosphatase, non-receptor type 12 cfa
CHICKEN:GGA.8364.1.S1_AT similar to protein tyrosine phosphatase, non-receptor type 12; protein-tyrosine phosphatase G1 gga
CHICKEN:GGAAFFX.22531.1.S1_AT similar to protein tyrosine phosphatase, non-receptor type 12; protein-tyrosine phosphatase G1 gga
HG-U95AV2:1463_AT protein tyrosine phosphatase, non-receptor type 12 hs
HC-G110:1463_AT protein tyrosine phosphatase, non-receptor type 12 hs
HUGENEFL:M93425_AT protein tyrosine phosphatase, non-receptor type 12 hs
HG-U133A:202006_AT protein tyrosine phosphatase, non-receptor type 12 hs
HG-U133_PLUS_2:202006_AT protein tyrosine phosphatase, non-receptor type 12 hs
HG-FOCUS:202006_AT protein tyrosine phosphatase, non-receptor type 12 hs
HG-U133A_2:202006_AT protein tyrosine phosphatase, non-receptor type 12 hs
U133_X3P:G4506286_3P_AT protein tyrosine phosphatase, non-receptor type 12 hs
U133_X3P:HS.62.1.S1_3P_A_AT protein tyrosine phosphatase, non-receptor type 12 hs
HG-U133A_2:216915_S_AT protein tyrosine phosphatase, non-receptor type 12 hs
HG-U133_PLUS_2:216915_S_AT protein tyrosine phosphatase, non-receptor type 12 hs
HG-U133A:216915_S_AT protein tyrosine phosphatase, non-receptor type 12 hs
HG-U133_PLUS_2:216884_AT protein tyrosine phosphatase, non-receptor type 12 hs
HG-U133A_2:216884_AT protein tyrosine phosphatase, non-receptor type 12 hs
HG-U133A:216884_AT protein tyrosine phosphatase, non-receptor type 12 hs
HG-U133_PLUS_2:244356_AT Protein tyrosine phosphatase, non-receptor type 12 hs
HG-U133B:244356_AT Protein tyrosine phosphatase, non-receptor type 12 hs
HU35KSUBB:RC_AA035649_AT Protein tyrosine phosphatase, non-receptor type 12 hs
U133_X3P:HS.293096.0.S1_3P_AT Protein tyrosine phosphatase, non-receptor type 12 hs
MOUSE430_2:1455105_AT protein tyrosine phosphatase, non-receptor type 12 mm
MOE430A:1455105_AT protein tyrosine phosphatase, non-receptor type 12 mm
MOUSE430A_2:1455105_AT protein tyrosine phosphatase, non-receptor type 12 mm
MOUSE430_2:1450478_A_AT protein tyrosine phosphatase, non-receptor type 12 mm
MOE430A:1450478_A_AT protein tyrosine phosphatase, non-receptor type 12 mm
MOUSE430A_2:1450478_A_AT protein tyrosine phosphatase, non-receptor type 12 mm
MU11KSUBB:X63440_S_AT protein tyrosine phosphatase, non-receptor type 12 mm
MG-U74AV2:102840_AT protein tyrosine phosphatase, non-receptor type 12 mm
MOE430A:1450479_X_AT protein tyrosine phosphatase, non-receptor type 12 mm
MOUSE430A_2:1450479_X_AT protein tyrosine phosphatase, non-receptor type 12 mm
MOUSE430_2:1450479_X_AT protein tyrosine phosphatase, non-receptor type 12 mm
MOE430A:1422045_A_AT protein tyrosine phosphatase, non-receptor type 12 mm
MOUSE430A_2:1422045_A_AT protein tyrosine phosphatase, non-receptor type 12 mm
MOUSE430_2:1422045_A_AT protein tyrosine phosphatase, non-receptor type 12 mm
MOE430B:1439705_AT Protein tyrosine phosphatase, non-receptor type 12 (Ptpn12), mRNA mm
MOUSE430_2:1439705_AT Protein tyrosine phosphatase, non-receptor type 12 (Ptpn12), mRNA mm
MG-U74CV2:138106_AT Protein tyrosine phosphatase, non-receptor type 12 (Ptpn12), mRNA mm
MOE430B:1459459_AT Protein tyrosine phosphatase, non-receptor type 12 (Ptpn12), mRNA mm
MOUSE430_2:1459459_AT Protein tyrosine phosphatase, non-receptor type 12 (Ptpn12), mRNA mm
MU19KSUBC:TC37721_S_AT Protein tyrosine phosphatase, non-receptor type 12 (Ptpn12), mRNA mm
Protein Similarities
Method ID Description E-Value
blast AAK68455 Hypothetical protein Y41D4A.5 [Caenorhabditis elegans] ref|NP_500128.1| Y41D4A.5 [Caenorhabditis elegans] 0.0
blast AAK68456 Hypothetical protein Y41D4A.6 [Caenorhabditis elegans] ref|NP_500129.1| Y41D4A.6 [Caenorhabditis elegans] 0.0
blast CAE63839 Hypothetical protein CBG08395 [Caenorhabditis briggsae] 1.0E-166
blast AAK68455 Hypothetical protein Y41D4A.5 [Caenorhabditis elegans] ref|NP_500128.1| Y41D4A.5 [Caenorhabditis elegans] 1.0E-138
blast CAE63838 Hypothetical protein CBG08394 [Caenorhabditis briggsae] 1.0E-130
blast AAK68455 Hypothetical protein Y41D4A.5 [Caenorhabditis elegans] ref|NP_500128.1| Y41D4A.5 [Caenorhabditis elegans] 8.0E-94
blast CAE63838 Hypothetical protein CBG08394 [Caenorhabditis briggsae] 2.0E-69
blast AAH58051 Protein tyrosine phosphatase, non-receptor type 12 [Danio rerio] ref|NP_956963.1| protein tyrosine phosphatase, non-receptor type 12 [Danio rerio] 3.0E-36
Protein Domains
Database ID Description E-Value
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 1.3E-62
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 1.1E-78
Pfam IPR000120 EMBL-EBI Amidase 1.4E-105
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 1.3E-51
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000028269 1 209-231
Sequence
Target Sequence 
>C. ELEGANS:175530_S_AT
cgagcatcgtgtctcactagtggtaattctgtgtaaactagtcgagttgaacaagataaa
atgcgaaagatactggccagaacaagtcggtgaaagtgaacttttcggtgattacgagat
cactttagaagaggagaaactctttgacgatgatgaatatttaatgagatgtctaaaaat
ggagaatcaaacaacaggagaatgtcgaaaagttcatcaacttcattatcgagaatggcc
agatcatgga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGAGCATCGTGTCTCACTAGTGGTA 339 249 13 Antisense
GCATCGTGTCTCACTAGTGGTAATT 384 309 16 Antisense
GGTAATTCTGTGTAAACTAGTCGAG 174 503 34 Antisense
AAATGCGAAAGATACTGGCCAGAAC 533 117 71 Antisense
GATACTGGCCAGAACAAGTCGGTGA 126 425 81 Antisense
GAAAGTGAACTTTTCGGTGATTACG 641 359 104 Antisense
GATTACGAGATCACTTTAGAAGAGG 79 427 122 Antisense
GAGGAGAAACTCTTTGACGATGATG 451 403 143 Antisense
GGAGAATGTCGAAAAGTTCATCAAC 582 519 209 Antisense
GTTCATCAACTTCATTATCGAGAAT 442 443 224 Antisense
TTATCGAGAATGGCCAGATCATGGA 218 669 238 Antisense
Sequence Source Affymetrix Proprietary Database