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[193160_s_at]

Description F56D1.4 /REP_DB=WormBase Gene ID /WP=CE26369 /GEN=clr-1 /TR=Q10118 /GB=AAA81098.2 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=protein-tyrosine-phosphatase
Cluster 6grp_highest_10_10 > 62      6grp_high1_10_10 > 26      4grp_highest_8_8 > 58      4grp_high_8_8 > 33      6grp_highest_nonorm > 30      6grp_total > 27      4grp_total > 38      6grp_highest_sub > Cu      6grp_cgc > 14      6grp_high1_sub > De      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 301
1 2 3 4 range
A 816.6
(3)
P 		629.4
(-0.7)
P 		515.5
(-3)
P 		528
(-2.8)
P 		301
B 797.2
(3)
P 		592.3
(-1.7)
P 		536.6
(-3)
P 		654.1
(-0.3)
P 		261
C 780.5
(3)
P 		641.6
(-1.4)
P 		597
(-2.8)
P 		589.3
(-3)
P 		191
avr 798.1
(3) 		621.1
(-1.3) 		549.7
(-3) 		590.5
(-2) 		248

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 626
1 2 3 4 5 6 range
A 934.3
(3)
P 		927.9
(2.9)
P 		609.9
(-3)
P 		610.7
(-3)
P 		681.3
(-1.7)
P 		801.7
(0.5)
P 		324
B 1009.9
(3)
P 		934.3
(2)
P 		634.1
(-2.1)
P 		832
(0.6)
P 		571.8
(-3)
P 		840.2
(0.7)
P 		438
C 1133.6
(3)
P 		980
(1.5)
P 		624.5
(-1.9)
P 		555.7
(-2.5)
P 		507.9
(-3)
P 		684
(-1.3)
P 		626
avr 1025.9
(3) 		947.4
(1.9) 		622.8
(-2.5) 		666.1
(-1.9) 		587
(-3) 		775.3
(-0.4) 		439
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 220
1 2 3 4 range
A 297.3
(3)
P 		136.6
(-1.4)
P 		134.8
(-1.4)
P 		77.3
(-3)
P 		220
B 254.2
(3)
P 		146.3
(-2)
P 		124.3
(-3)
P 		139.4
(-2.3)
P 		130
C 258.4
(3)
P 		184.5
(0.2)
P 		208.1
(1.1)
P 		99.4
(-3)
P 		159
avr 270
(3) 		155.8
(-1.2) 		155.7
(-1.2) 		105.4
(-3) 		165

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 309
1 2 3 4 5 6 range
A 172.2
(-1.8)
P 		330
(3)
P 		132.8
(-3)
P 		154.9
(-2.3)
P 		205.6
(-0.8)
P 		195.2
(-1.1)
P 		197
B 351.4
(3)
P 		311
(1.8)
P 		154
(-3)
P 		220.4
(-1)
P 		232.3
(-0.6)
P 		313.3
(1.8)
P 		197
C 420.2
(3)
P 		299
(0.6)
P 		159
(-2.1)
P 		111.7
(-3)
P 		164.4
(-2)
P 		229
(-0.7)
P 		309
avr 314.6
(3) 		313.3
(3) 		148.6
(-3) 		162.3
(-2.5) 		200.8
(-1.1) 		245.8
(0.5) 		166
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193160_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4968
Sequence Type Exemplar sequence
Representative Public ID F56D1.4 NCBI
Target Description F56D1.4 /REP_DB=WormBase Gene ID /WP=CE26369 /GEN=clr-1 /TR=Q10118 /GB=AAA81098.2 /SUBMIT=ST.LOUIS /CHR=2 /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_001027037(11), NM_001027039(11), NM_001027038(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027037 NCBI Caenorhabditis elegans CLeaR family member (clr-1) (clr-1) mRNA, complete cds. 11/11 None
NM_001027039 NCBI Caenorhabditis elegans CLeaR family member (clr-1) (clr-1) mRNA, complete cds. 11/11 None
NM_001027038 NCBI Caenorhabditis elegans CLeaR family member (clr-1) (clr-1) mRNA, complete cds. 11/11 None
GENEFINDER00000013103 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:5466444:5475260:1 11/11 None
F56D1.4c ENSEMBL cdna:known chromosome:CEL140:II:5466335:5473770:1 gene:F56D1.4 11/11 A 
F56D1.4a ENSEMBL cdna:known chromosome:CEL140:II:5466335:5473770:1 gene:F56D1.4 11/11 A 
F56D1.4b ENSEMBL cdna:known chromosome:CEL140:II:5466444:5473760:1 gene:F56D1.4 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000013099 7/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:5466441-5473353(+) 100.0 100.0
Public Domain and Genome References
Ensembl F56D1.4
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAN60515 Clear protein 1, isoform a [Caenorhabditis elegans] ref|NP_001022208.1| CLeaR family member (clr-1) [Caenorhabditis elegans] 0.0
blast AAC27551 CLR-1 [Caenorhabditis elegans] 0.0
blast AAN60516 Clear protein 1, isoform b [Caenorhabditis elegans] ref|NP_001022209.1| CLeaR family member (clr-1) [Caenorhabditis elegans] 0.0
blast AAN60517 Clear protein 1, isoform c [Caenorhabditis elegans] ref|NP_001022210.1| CLeaR family member (clr-1) [Caenorhabditis elegans] 0.0
blast AAC27552 truncated CLR-1 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 6.6E-109
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 3.8E-81
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 6.6E-109
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 3.8E-81
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 4.8E-51
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 6.6E-109
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 3.8E-81
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001022210.1 1 719-738
F56D1.4c 1 719-738
Sequence
Target Sequence 
>C. ELEGANS:193160_S_AT
tagccgctcaggatcctgtttcagaaggaacagcttttgatttctggagaatgattgctg
atcaaaatgtgactacggtagttatgttgagtgatgagacagattggagtgatgttgaaa
agtactggccaatcgatggttctggaacagaatgtcactttggatcggaacgtaattcag
tgaatgttacctgtgtctctgaagagcaccatcaagattttatcattcgaaatttatcat
attctatgaaagataacgaatcgatgccagcgaaccaagaagttgtacagtattcgtata
ctggatggccttcggattcaattgttccaaaatctgcgaacagtttgatgaatctgattg
agatggtcctgcaacgtcagagcagtctcatgggatctcaggctccgattgtggtacatt
gcagaaacggatcgtcagagagcggaatcttcatatgcatttccttgttatggctccgac
aaaaagctgaacaacggatagacgtcttccaaacagtaaaaggacttcaatcacaccgac
cgatgatgtttacccgttttgagcagtattctttct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TAGCCGCTCAGGATCCTGTTTCAGA 371 651 3617 Antisense
AGTACTGGCCAATCGATGGTTCTGG 186 61 3737 Antisense
GTGAATGTTACCTGTGTCTCTGAAG 506 481 3796 Antisense
GGATGGCCTTCGGATTCAATTGTTC 113 515 3919 Antisense
GATTGAGATGGTCCTGCAACGTCAG 218 433 3972 Antisense
GAGCAGTCTCATGGGATCTCAGGCT 602 389 3996 Antisense
ATCTCAGGCTCCGATTGTGGTACAT 495 31 4011 Antisense
TATGCATTTCCTTGTTATGGCTCCG 211 657 4070 Antisense
TAAAAGGACTTCAATCACACCGACC 21 639 4133 Antisense
CACCGACCGATGATGTTTACCCGTT 306 191 4150 Antisense
ACCCGTTTTGAGCAGTATTCTTTCT 200 35 4168 Antisense
Sequence Source Affymetrix Proprietary Database