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[177338_at]

Description CD4.1 /REP_DB=WormBase Gene ID /WP=CE16949 /TR=O44162 /GB=AAB88339.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_high1_10_10 > 25      4grp_high_8_8 > 28      6grp_total > 26      4grp_total > 19      6grp_high1_sub > 01_02      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 160
1 2 3 4 range
A 91.9
(-2.6)
P 		160.9
(0.1)
P 		82.2
(-3)
A 		236
(3)
P 		154
B 144.9
(2.7)
P 		127.8
(1.1)
A 		84.9
(-3)
A 		148
(3)
P 		63
C 107
(-1.5)
P 		113.6
(-1.1)
A 		75.6
(-3)
P 		198.3
(3)
P 		123
avr 114.6
(-1.2) 		134.1
(-0.2) 		80.9
(-3) 		194.1
(3) 		113

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 90
1 2 3 4 5 6 range
A 136.5
(3)
P 		123.8
(1.8)
P 		79.3
(-2.4)
P 		119.6
(1.4)
P 		73
(-3)
P 		85.3
(-1.8)
P 		64
B 120.3
(3)
P 		120.8
(3)
P 		85.3
(-0.2)
P 		74.6
(-1.2)
A 		86.1
(-0.2)
A 		55
(-3)
P 		66
C 140.8
(2.7)
P 		144.7
(3)
P 		72.3
(-2.9)
P 		78.6
(-2.4)
A 		70.9
(-3)
M 		110.7
(0.2)
P 		74
avr 132.5
(3) 		129.8
(2.7) 		79
(-2.8) 		90.9
(-1.5) 		76.7
(-3) 		83.7
(-2.2) 		56
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 27
1 2 3 4 range
A 33.5
(2.4)
P 		34.9
(3)
P 		21.5
(-3)
A 		34.5
(2.8)
P 		13
B 46.2
(3)
P 		31.6
(-0.3)
A 		19.7
(-3)
A 		31.5
(-0.3)
P 		27
C 35.4
(3)
P 		32.7
(1.2)
A 		26.4
(-3)
P 		33.4
(1.7)
P 		9
avr 38.4
(3) 		33.1
(1) 		22.5
(-3) 		33.1
(1) 		16

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 36
1 2 3 4 5 6 range
A 25.2
(-1.2)
P 		44
(3)
P 		17.3
(-3)
P 		30.3
(-0.1)
P 		22
(-1.9)
P 		20.8
(-2.2)
P 		27
B 41.9
(3)
P 		40.2
(2.5)
P 		20.7
(-2.8)
P 		19.8
(-3)
A 		35
(1.1)
A 		20.5
(-2.8)
P 		22
C 52.2
(3)
P 		44.2
(1.7)
P 		18.4
(-2.6)
P 		15.8
(-3)
A 		22.9
(-1.8)
M 		37
(0.5)
P 		36
avr 39.8
(2.3) 		42.8
(3) 		18.8
(-3) 		22
(-2.2) 		26.6
(-1.1) 		26.1
(-1.2) 		24
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 177338_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11587
Sequence Type Exemplar sequence
Representative Public ID CD4.1 NCBI
Target Description CD4.1 /REP_DB=WormBase Gene ID /WP=CE16949 /TR=O44162 /GB=AAB88339.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=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_072078(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072078 NCBI Caenorhabditis elegans CD4.1 (CD4.1) mRNA, complete cds. 11/11 None
GENEFINDER00000006246 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:5609895:5611841:1 9/11 None
CD4.1 ENSEMBL cdna:known chromosome:CEL140:V:5609789:5611502:1 gene:CD4.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000006237 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:5609788-5611502(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl CD4.1
Entrez Gene 183875 Entrez gene
SwissProt O44162 EMBL-EBI
WormBase CE16949 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAE64604 Hypothetical protein CBG09360 [Caenorhabditis briggsae] 3.0E-88
blast NP_504479 CD4.1 [Caenorhabditis elegans] gb|AAB88339.1| Hypothetical protein CD4.1 [Caenorhabditis elegans] 7.0E-69
blast NP_504479 CD4.1 [Caenorhabditis elegans] gb|AAB88339.1| Hypothetical protein CD4.1 [Caenorhabditis elegans] 2.0E-55
blast CAE64604 Hypothetical protein CBG09360 [Caenorhabditis briggsae] 2.0E-37
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_504479.1 1 67-89
CD4.1 1 67-89
GENEFINDER00000006246 1 48-70
Sequence
Target Sequence 
>C. ELEGANS:177338_AT
agaagtttattagacatgccgggatcaacagatcaagaaaatcacatgactggatatgaa
ccaccacaagggaactcagatagtggcttgacggagcatcgaacacatcaatatataaat
cgcccagaaggagaaatggatatgatgataggattcttcttgatgaatggattttgtgtt
tccttcttcctcctcttcggtctctgcgtgatattctcctgtctccgaaaacgaccatcc
tatttccgaaggaagcaattttccgagactgaaaatgtggtcccagttcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGAAGTTTATTAGACATGCCGGGAT 248 75 55 Antisense
TAGACATGCCGGGATCAACAGATCA 86 653 65 Antisense
CACATGACTGGATATGAACCACCAC 358 183 97 Antisense
GAACCACCACAAGGGAACTCAGATA 522 345 112 Antisense
GGAACTCAGATAGTGGCTTGACGGA 667 529 125 Antisense
GCTTGACGGAGCATCGAACACATCA 256 307 140 Antisense
ACACATCAATATATAAATCGCCCAG 57 111 157 Antisense
TATTCTCCTGTCTCCGAAAACGACC 517 661 266 Antisense
GAAAACGACCATCCTATTTCCGAAG 239 351 281 Antisense
GAAGGAAGCAATTTTCCGAGACTGA 284 333 302 Antisense
GACTGAAAATGTGGTCCCAGTTCAA 70 375 321 Antisense
Sequence Source Affymetrix Proprietary Database